Fiber-seq toolkit in rust
Usage: ft [OPTIONS] <COMMAND>
Commands:
predict-m6a Predict m6A positions using HiFi kinetics data and encode the results in the MM
and ML bam tags. Also adds nucleosome (nl, ns) and MTase sensitive patches (al,
as) [aliases: m6A, m6a]
add-nucleosomes Add nucleosomes to a bam file with m6a predictions
fire Add FIREs (Fiber-seq Inferred Regulatory Elements) to a bam file with m6a
predictions
extract Extract fiberseq data into plain text files [aliases: ex, e]
center This command centers fiberseq data around given reference positions. This is
useful for making aggregate m6A and CpG observations, as well as visualization
of SVs [aliases: c, ct]
footprint Infer footprints from fiberseq data
qc Collect QC metrics from a fiberseq bam file
track-decorators Make decorated bed files for fiberseq data
pileup Make a pileup track of Fiber-seq features from a FIRE bam
clear-kinetics Remove HiFi kinetics tags from the input bam file
convert-tags Convert legacy (lowercase) fiberseq tags to MA spec
strip-basemods Strip out select base modifications
ddda-to-m6a Convert a DddA BAM file to pseudo m6A BAM file
fiber-hmm Apply FiberHMM to a bam file
validate Validate a Fiber-seq BAM file for m6A, nucleosome, and optionally FIRE calls
pg-inject Create a mock BAM file from a reference FASTA with perfectly aligned sequences
pg-lift Lift annotations through a pangenome graph from source to target coordinates
pg-pansn Add or strip panSN-spec prefixes from BAM contig names
call-peaks Call FIRE peaks using FDR-based peak calling on pileup data [aliases: peaks,
call]
mock-fire Create a mock BAM file with FIRE elements from a BED file. Each interval in the
BED becomes a FIRE element. The 4th column groups intervals into the same mock
read
help Print this message or the help of the given subcommand(s)
Options:
-h, --help Print help
-V, --version Print version
Global-Options:
-t, --threads <THREADS> Threads [default: 8]
Debug-Options:
-v, --verbose... Logging level [-v: Info, -vv: Debug, -vvv: Trace]
--quiet Turn off all logging
Predict m6A positions using HiFi kinetics data and encode the results in the MM and ML bam tags.
Also adds nucleosome (nl, ns) and MTase sensitive patches (al, as)
Usage: ft predict-m6a [OPTIONS] [BAM] [OUT]
Arguments:
[BAM] Input BAM file. If no path is provided stdin is used. For m6A prediction, this should be a
HiFi bam file with kinetics data. For other commands, this should be a bam file with m6A
calls [default: -]
[OUT] Output bam file with m6A calls in new/extended MM and ML bam tags [default: -]
Options:
-n, --nucleosome-length <NUCLEOSOME_LENGTH>
Minium nucleosome length [default: 75]
-c, --combined-nucleosome-length <COMBINED_NUCLEOSOME_LENGTH>
Minium nucleosome length when combining over a single m6A [default: 100]
--min-distance-added <MIN_DISTANCE_ADDED>
Minium distance needed to add to an already existing nuc by crossing an m6a [default: 25]
-d, --distance-from-end <DISTANCE_FROM_END>
Minimum distance from the end of a fiber to call a nucleosome or MSP [default: 45]
-k, --keep
Keep hifi kinetics data
-h, --help
Print help (see more with '--help')
-V, --version
Print version
BAM-Options:
-F, --filter <BIT_FLAG> BAM bit flags to filter on, equivalent to `-F` in samtools view
Defaults to 0 (no filtering)
-x, --ftx <FILTER_EXPRESSION> Filtering expression to use for filtering records Example: filter
to nucleosomes with lengths greater than 150 bp -x "len(nuc)>150"
Example: filter to msps with lengths between 30 and 49 bp -x
"len(msp)=30:50" Example: combine 2+ filter expressions -x
"len(nuc)<150,len(msp)=30:50" Filtering expressions support len()
and qual() functions over msp, nuc, m6a, cpg
--ml <MIN_ML_SCORE> Minium score in the ML tag to use or include in the output [env:
FT_MIN_ML_SCORE=] [default: 125]
-u, --uncompressed Output uncompressed BAM files
FIRE-Filter:
--fire-filter
Convenience: apply the FIRE peak-calling pipeline's fiber-level filters (`--skip-no-m6a`,
`--min-msp 10`, `--min-ave-msp-size 10`). Individual filter flags still override when both
are set. Requires MSP/m6A annotations on the input BAM, so it is a no-op for commands that
run before those annotations exist
--skip-no-m6a[=<SKIP_NO_M6A>]
Drop fibers with no m6A calls. Off by default; `--fire-filter` turns this on unless
explicitly set to `false`. Use `--skip-no-m6a=false` to override when `--fire-filter` is
set [possible values: true, false]
--min-msp <MIN_MSP>
Drop fibers with fewer than `N` MSP calls. Off (0) by default; `--fire-filter` sets this
to 10 unless overridden [env: MIN_MSP=]
--min-ave-msp-size <MIN_AVE_MSP_SIZE>
Drop fibers whose average MSP size is below `N`. Off (0) by default; `--fire-filter` sets
this to 10 unless overridden [env: MIN_AVE_MSP_SIZE=]
Global-Options:
-t, --threads <THREADS> Threads [default: 8]
Debug-Options:
-v, --verbose... Logging level [-v: Info, -vv: Debug, -vvv: Trace]
--quiet Turn off all logging
Developer-Options:
--force-min-ml-score <FORCE_MIN_ML_SCORE>
Force a different minimum ML score
--all-calls
Keep all m6A calls regardless of how low the ML value is
-b, --batch-size <BATCH_SIZE>
Number of reads to include in batch prediction [default: 1]
Add nucleosomes to a bam file with m6a predictions
Usage: ft add-nucleosomes [OPTIONS] [BAM] [OUT]
Arguments:
[BAM] Input BAM file. If no path is provided stdin is used. For m6A prediction, this should be a
HiFi bam file with kinetics data. For other commands, this should be a bam file with m6A
calls [default: -]
[OUT] Output bam file with nucleosome calls [default: -]
Options:
-n, --nucleosome-length <NUCLEOSOME_LENGTH>
Minium nucleosome length [default: 75]
-c, --combined-nucleosome-length <COMBINED_NUCLEOSOME_LENGTH>
Minium nucleosome length when combining over a single m6A [default: 100]
--min-distance-added <MIN_DISTANCE_ADDED>
Minium distance needed to add to an already existing nuc by crossing an m6a [default: 25]
-d, --distance-from-end <DISTANCE_FROM_END>
Minimum distance from the end of a fiber to call a nucleosome or MSP [default: 45]
-h, --help
Print help
-V, --version
Print version
BAM-Options:
-F, --filter <BIT_FLAG> BAM bit flags to filter on, equivalent to `-F` in samtools view
Defaults to 0 (no filtering)
-x, --ftx <FILTER_EXPRESSION> Filtering expression to use for filtering records Example: filter
to nucleosomes with lengths greater than 150 bp -x "len(nuc)>150"
Example: filter to msps with lengths between 30 and 49 bp -x
"len(msp)=30:50" Example: combine 2+ filter expressions -x
"len(nuc)<150,len(msp)=30:50" Filtering expressions support len()
and qual() functions over msp, nuc, m6a, cpg
--ml <MIN_ML_SCORE> Minium score in the ML tag to use or include in the output [env:
FT_MIN_ML_SCORE=] [default: 125]
-u, --uncompressed Output uncompressed BAM files
FIRE-Filter:
--fire-filter
Convenience: apply the FIRE peak-calling pipeline's fiber-level filters (`--skip-no-m6a`,
`--min-msp 10`, `--min-ave-msp-size 10`). Individual filter flags still override when both
are set. Requires MSP/m6A annotations on the input BAM, so it is a no-op for commands that
run before those annotations exist
--skip-no-m6a[=<SKIP_NO_M6A>]
Drop fibers with no m6A calls. Off by default; `--fire-filter` turns this on unless
explicitly set to `false`. Use `--skip-no-m6a=false` to override when `--fire-filter` is
set [possible values: true, false]
--min-msp <MIN_MSP>
Drop fibers with fewer than `N` MSP calls. Off (0) by default; `--fire-filter` sets this
to 10 unless overridden [env: MIN_MSP=]
--min-ave-msp-size <MIN_AVE_MSP_SIZE>
Drop fibers whose average MSP size is below `N`. Off (0) by default; `--fire-filter` sets
this to 10 unless overridden [env: MIN_AVE_MSP_SIZE=]
Global-Options:
-t, --threads <THREADS> Threads [default: 8]
Debug-Options:
-v, --verbose... Logging level [-v: Info, -vv: Debug, -vvv: Trace]
--quiet Turn off all logging
Add FIREs (Fiber-seq Inferred Regulatory Elements) to a bam file with m6a predictions
Usage: ft fire [OPTIONS] [BAM] [OUT]
Arguments:
[BAM] Input BAM file. If no path is provided stdin is used. For m6A prediction, this should be a
HiFi bam file with kinetics data. For other commands, this should be a bam file with m6A
calls [default: -]
[OUT] Output file (BAM by default, table of MSP features if `--feats-to-text` is used, and bed9 +
if `--extract`` is used) [default: -]
Options:
--ont
Force the ONT heuristic adjustment for every read in FIRE calling. This adjusts the
observed number of m6A counts by adding pseudo counts to account for the single stranded
nature of ONT data. ONT reads are auto-detected per read (via aux tags / read name), so
this flag is only needed to override detection; reads matching no known platform
convention default to PacBio [env: ONT=]
-e, --extract
Output just FIRE elements in bed9 format
--all
When extracting bed9 format include all MSPs and nucleosomes
-f, --feats-to-text
Output FIREs features for training in a table format
-w, --width-bin <WIDTH_BIN>
Width of bin for feature collection [env: WIDTH_BIN=] [default: 40]
-b, --bin-num <BIN_NUM>
Number of bins to collect [env: BIN_NUM=] [default: 9]
--best-window-size <BEST_WINDOW_SIZE>
Calculate stats for the highest X bp window within each MSP Should be a fair amount higher
than the expected linker length [env: BEST_WINDOW_SIZE=] [default: 100]
--min-msp-length-for-positive-fire-call <MIN_MSP_LENGTH_FOR_POSITIVE_FIRE_CALL>
Minium length of msp to call a FIRE [env: MIN_MSP_LENGTH_FOR_POSITIVE_FIRE_CALL=]
[default: 85]
--model <MODEL>
Optional path to a model json file. If not provided ft will use the default model
(recommended) [env: FIRE_MODEL=]
--fdr-table <FDR_TABLE>
Optional path to a FDR table [env: FDR_TABLE=]
-h, --help
Print help
-V, --version
Print version
BAM-Options:
-F, --filter <BIT_FLAG> BAM bit flags to filter on, equivalent to `-F` in samtools view
Defaults to 0 (no filtering)
-x, --ftx <FILTER_EXPRESSION> Filtering expression to use for filtering records Example: filter
to nucleosomes with lengths greater than 150 bp -x "len(nuc)>150"
Example: filter to msps with lengths between 30 and 49 bp -x
"len(msp)=30:50" Example: combine 2+ filter expressions -x
"len(nuc)<150,len(msp)=30:50" Filtering expressions support len()
and qual() functions over msp, nuc, m6a, cpg
--ml <MIN_ML_SCORE> Minium score in the ML tag to use or include in the output [env:
FT_MIN_ML_SCORE=] [default: 125]
-u, --uncompressed Output uncompressed BAM files
FIRE-Filter:
--fire-filter
Convenience: apply the FIRE peak-calling pipeline's fiber-level filters (`--skip-no-m6a`,
`--min-msp 10`, `--min-ave-msp-size 10`). Individual filter flags still override when both
are set. Requires MSP/m6A annotations on the input BAM, so it is a no-op for commands that
run before those annotations exist
--skip-no-m6a[=<SKIP_NO_M6A>]
Drop fibers with no m6A calls. Off by default; `--fire-filter` turns this on unless
explicitly set to `false`. Use `--skip-no-m6a=false` to override when `--fire-filter` is
set [possible values: true, false]
--min-msp <MIN_MSP>
Drop fibers with fewer than `N` MSP calls. Off (0) by default; `--fire-filter` sets this
to 10 unless overridden [env: MIN_MSP=]
--min-ave-msp-size <MIN_AVE_MSP_SIZE>
Drop fibers whose average MSP size is below `N`. Off (0) by default; `--fire-filter` sets
this to 10 unless overridden [env: MIN_AVE_MSP_SIZE=]
Global-Options:
-t, --threads <THREADS> Threads [default: 8]
Debug-Options:
-v, --verbose... Logging level [-v: Info, -vv: Debug, -vvv: Trace]
--quiet Turn off all logging
Extract fiberseq data into plain text files
Usage: ft extract [OPTIONS] [BAM]
Arguments:
[BAM] Input BAM file. If no path is provided stdin is used. For m6A prediction, this should be a
HiFi bam file with kinetics data. For other commands, this should be a bam file with m6A
calls [default: -]
Options:
-r, --reference Report positions in reference sequence coordinates
--molecular Report positions in the molecular sequence coordinates
--m6a <M6A> Output path for m6a bed12
-c, --cpg <CPG> Output path for 5mC (CpG, primrose) bed12
--msp <MSP> Output path for methylation sensitive patch (msp) bed12
-n, --nuc <NUC> Output path for nucleosome bed12
-a, --all <ALL> Output path for a tabular format including "all" fiberseq information in the bam
-h, --help Print help (see more with '--help')
-V, --version Print version
BAM-Options:
-F, --filter <BIT_FLAG> BAM bit flags to filter on, equivalent to `-F` in samtools view
Defaults to 0 (no filtering)
-x, --ftx <FILTER_EXPRESSION> Filtering expression to use for filtering records Example: filter
to nucleosomes with lengths greater than 150 bp -x "len(nuc)>150"
Example: filter to msps with lengths between 30 and 49 bp -x
"len(msp)=30:50" Example: combine 2+ filter expressions -x
"len(nuc)<150,len(msp)=30:50" Filtering expressions support len()
and qual() functions over msp, nuc, m6a, cpg
--ml <MIN_ML_SCORE> Minium score in the ML tag to use or include in the output [env:
FT_MIN_ML_SCORE=] [default: 125]
-u, --uncompressed Output uncompressed BAM files
FIRE-Filter:
--fire-filter
Convenience: apply the FIRE peak-calling pipeline's fiber-level filters (`--skip-no-m6a`,
`--min-msp 10`, `--min-ave-msp-size 10`). Individual filter flags still override when both
are set. Requires MSP/m6A annotations on the input BAM, so it is a no-op for commands that
run before those annotations exist
--skip-no-m6a[=<SKIP_NO_M6A>]
Drop fibers with no m6A calls. Off by default; `--fire-filter` turns this on unless
explicitly set to `false`. Use `--skip-no-m6a=false` to override when `--fire-filter` is
set [possible values: true, false]
--min-msp <MIN_MSP>
Drop fibers with fewer than `N` MSP calls. Off (0) by default; `--fire-filter` sets this
to 10 unless overridden [env: MIN_MSP=]
--min-ave-msp-size <MIN_AVE_MSP_SIZE>
Drop fibers whose average MSP size is below `N`. Off (0) by default; `--fire-filter` sets
this to 10 unless overridden [env: MIN_AVE_MSP_SIZE=]
Global-Options:
-t, --threads <THREADS> Threads [default: 8]
Debug-Options:
-v, --verbose... Logging level [-v: Info, -vv: Debug, -vvv: Trace]
--quiet Turn off all logging
All-Format-Options:
-q, --quality Include per base quality scores in "fiber_qual"
-s, --simplify Simplify output by removing fiber sequence
This command centers fiberseq data around given reference positions. This is useful for making
aggregate m6A and CpG observations, as well as visualization of SVs
Usage: ft center [OPTIONS] --bed <BED> [BAM]
Arguments:
[BAM] Input BAM file. If no path is provided stdin is used. For m6A prediction, this should be a
HiFi bam file with kinetics data. For other commands, this should be a bam file with m6A
calls [default: -]
Options:
-b, --bed <BED> Bed file on which to center fiberseq reads. Data is adjusted to the start
position of the bed file and corrected for strand if the strand is indicated in
the 6th column of the bed file. The 4th column will also be checked for the
strand but only after the 6th is. If you include strand information in the 4th
(or 6th) column it will orient data accordingly and use the end position of bed
record instead of the start if on the minus strand. This means that profiles of
motifs in both the forward and minus orientation will align to the same central
position
-d, --dist <DIST> Set a maximum distance from the start of the motif to keep a feature
-w, --wide Provide data in wide format, one row per read
-r, --reference Return relative reference position instead of relative molecular position
-s, --simplify Replace the sequence output column with just "N"
-h, --help Print help (see more with '--help')
-V, --version Print version
BAM-Options:
-F, --filter <BIT_FLAG> BAM bit flags to filter on, equivalent to `-F` in samtools view
Defaults to 0 (no filtering)
-x, --ftx <FILTER_EXPRESSION> Filtering expression to use for filtering records Example: filter
to nucleosomes with lengths greater than 150 bp -x "len(nuc)>150"
Example: filter to msps with lengths between 30 and 49 bp -x
"len(msp)=30:50" Example: combine 2+ filter expressions -x
"len(nuc)<150,len(msp)=30:50" Filtering expressions support len()
and qual() functions over msp, nuc, m6a, cpg
--ml <MIN_ML_SCORE> Minium score in the ML tag to use or include in the output [env:
FT_MIN_ML_SCORE=] [default: 125]
-u, --uncompressed Output uncompressed BAM files
FIRE-Filter:
--fire-filter
Convenience: apply the FIRE peak-calling pipeline's fiber-level filters (`--skip-no-m6a`,
`--min-msp 10`, `--min-ave-msp-size 10`). Individual filter flags still override when both
are set. Requires MSP/m6A annotations on the input BAM, so it is a no-op for commands that
run before those annotations exist
--skip-no-m6a[=<SKIP_NO_M6A>]
Drop fibers with no m6A calls. Off by default; `--fire-filter` turns this on unless
explicitly set to `false`. Use `--skip-no-m6a=false` to override when `--fire-filter` is
set [possible values: true, false]
--min-msp <MIN_MSP>
Drop fibers with fewer than `N` MSP calls. Off (0) by default; `--fire-filter` sets this
to 10 unless overridden [env: MIN_MSP=]
--min-ave-msp-size <MIN_AVE_MSP_SIZE>
Drop fibers whose average MSP size is below `N`. Off (0) by default; `--fire-filter` sets
this to 10 unless overridden [env: MIN_AVE_MSP_SIZE=]
Global-Options:
-t, --threads <THREADS> Threads [default: 8]
Debug-Options:
-v, --verbose... Logging level [-v: Info, -vv: Debug, -vvv: Trace]
--quiet Turn off all logging
Infer footprints from fiberseq data
Usage: ft footprint [OPTIONS] --bed <BED> --yaml <YAML> [BAM]
Arguments:
[BAM] Input BAM file. If no path is provided stdin is used. For m6A prediction, this should be a
HiFi bam file with kinetics data. For other commands, this should be a bam file with m6A
calls [default: -]
Options:
-b, --bed <BED> BED file with the regions to footprint. Should all contain the same motif with
proper strand information, and ideally be ChIP-seq peaks
-y, --yaml <YAML> yaml describing the modules of the footprint
-o, --out <OUT> Output bam [default: -]
-h, --help Print help
-V, --version Print version
BAM-Options:
-F, --filter <BIT_FLAG> BAM bit flags to filter on, equivalent to `-F` in samtools view
Defaults to 0 (no filtering)
-x, --ftx <FILTER_EXPRESSION> Filtering expression to use for filtering records Example: filter
to nucleosomes with lengths greater than 150 bp -x "len(nuc)>150"
Example: filter to msps with lengths between 30 and 49 bp -x
"len(msp)=30:50" Example: combine 2+ filter expressions -x
"len(nuc)<150,len(msp)=30:50" Filtering expressions support len()
and qual() functions over msp, nuc, m6a, cpg
--ml <MIN_ML_SCORE> Minium score in the ML tag to use or include in the output [env:
FT_MIN_ML_SCORE=] [default: 125]
-u, --uncompressed Output uncompressed BAM files
FIRE-Filter:
--fire-filter
Convenience: apply the FIRE peak-calling pipeline's fiber-level filters (`--skip-no-m6a`,
`--min-msp 10`, `--min-ave-msp-size 10`). Individual filter flags still override when both
are set. Requires MSP/m6A annotations on the input BAM, so it is a no-op for commands that
run before those annotations exist
--skip-no-m6a[=<SKIP_NO_M6A>]
Drop fibers with no m6A calls. Off by default; `--fire-filter` turns this on unless
explicitly set to `false`. Use `--skip-no-m6a=false` to override when `--fire-filter` is
set [possible values: true, false]
--min-msp <MIN_MSP>
Drop fibers with fewer than `N` MSP calls. Off (0) by default; `--fire-filter` sets this
to 10 unless overridden [env: MIN_MSP=]
--min-ave-msp-size <MIN_AVE_MSP_SIZE>
Drop fibers whose average MSP size is below `N`. Off (0) by default; `--fire-filter` sets
this to 10 unless overridden [env: MIN_AVE_MSP_SIZE=]
Global-Options:
-t, --threads <THREADS> Threads [default: 8]
Debug-Options:
-v, --verbose... Logging level [-v: Info, -vv: Debug, -vvv: Trace]
--quiet Turn off all logging
Collect QC metrics from a fiberseq bam file
Usage: ft qc [OPTIONS] [BAM] [OUT]
Arguments:
[BAM] Input BAM file. If no path is provided stdin is used. For m6A prediction, this should be a
HiFi bam file with kinetics data. For other commands, this should be a bam file with m6A
calls [default: -]
[OUT] Output text file with QC metrics. The format is a tab-separated file with the following
columns: "statistic\tvalue\tcount" where "statistic" is the name of the metric, "value" is
the value of the metric, and "count" is the number of times the metric was observed
[default: -]
Options:
--acf
Calculate the auto-correlation function of the m6A marks in the fiber-seq data
--acf-max-lag <ACF_MAX_LAG>
maximum lag for the ACF calculation [default: 250]
--acf-min-m6a <ACF_MIN_M6A>
Minimum number of m6A marks to use a read in the ACF calculation [default: 100]
--acf-max-reads <ACF_MAX_READS>
maximum number of reads to use in the ACF calculation [default: 10000]
--acf-sample-rate <ACF_SAMPLE_RATE>
After sampling the first "acf-max-reads" randomly sample one of every "acf-sample-rate"
reads and replace one of the previous reads at random [default: 100]
-m, --m6a-per-msp
In the output include a measure of the number of m6A events per MSPs of a given size. The
output format is: "m6a_per_msp_size\t{m6A count},{MSP size},{is a FIRE}\t{count}" e.g.
"m6a_per_msp_size\t35,100,false\t100"
--n-reads <N_READS>
Only process the first "n" reads in the input bam file
-h, --help
Print help
-V, --version
Print version
BAM-Options:
-F, --filter <BIT_FLAG> BAM bit flags to filter on, equivalent to `-F` in samtools view
Defaults to 0 (no filtering)
-x, --ftx <FILTER_EXPRESSION> Filtering expression to use for filtering records Example: filter
to nucleosomes with lengths greater than 150 bp -x "len(nuc)>150"
Example: filter to msps with lengths between 30 and 49 bp -x
"len(msp)=30:50" Example: combine 2+ filter expressions -x
"len(nuc)<150,len(msp)=30:50" Filtering expressions support len()
and qual() functions over msp, nuc, m6a, cpg
--ml <MIN_ML_SCORE> Minium score in the ML tag to use or include in the output [env:
FT_MIN_ML_SCORE=] [default: 125]
-u, --uncompressed Output uncompressed BAM files
FIRE-Filter:
--fire-filter
Convenience: apply the FIRE peak-calling pipeline's fiber-level filters (`--skip-no-m6a`,
`--min-msp 10`, `--min-ave-msp-size 10`). Individual filter flags still override when both
are set. Requires MSP/m6A annotations on the input BAM, so it is a no-op for commands that
run before those annotations exist
--skip-no-m6a[=<SKIP_NO_M6A>]
Drop fibers with no m6A calls. Off by default; `--fire-filter` turns this on unless
explicitly set to `false`. Use `--skip-no-m6a=false` to override when `--fire-filter` is
set [possible values: true, false]
--min-msp <MIN_MSP>
Drop fibers with fewer than `N` MSP calls. Off (0) by default; `--fire-filter` sets this
to 10 unless overridden [env: MIN_MSP=]
--min-ave-msp-size <MIN_AVE_MSP_SIZE>
Drop fibers whose average MSP size is below `N`. Off (0) by default; `--fire-filter` sets
this to 10 unless overridden [env: MIN_AVE_MSP_SIZE=]
Global-Options:
-t, --threads <THREADS> Threads [default: 8]
Debug-Options:
-v, --verbose... Logging level [-v: Info, -vv: Debug, -vvv: Trace]
--quiet Turn off all logging
Make decorated bed files for fiberseq data
Usage: ft track-decorators [OPTIONS] --bed12 <BED12> [BAM]
Arguments:
[BAM] Input BAM file. If no path is provided stdin is used. For m6A prediction, this should be a
HiFi bam file with kinetics data. For other commands, this should be a bam file with m6A
calls [default: -]
Options:
-b, --bed12 <BED12> Output path for bed12 file to be decorated
-d, --decorator <DECORATOR> Output path for decorator bed file [default: -]
-h, --help Print help
-V, --version Print version
BAM-Options:
-F, --filter <BIT_FLAG> BAM bit flags to filter on, equivalent to `-F` in samtools view
Defaults to 0 (no filtering)
-x, --ftx <FILTER_EXPRESSION> Filtering expression to use for filtering records Example: filter
to nucleosomes with lengths greater than 150 bp -x "len(nuc)>150"
Example: filter to msps with lengths between 30 and 49 bp -x
"len(msp)=30:50" Example: combine 2+ filter expressions -x
"len(nuc)<150,len(msp)=30:50" Filtering expressions support len()
and qual() functions over msp, nuc, m6a, cpg
--ml <MIN_ML_SCORE> Minium score in the ML tag to use or include in the output [env:
FT_MIN_ML_SCORE=] [default: 125]
-u, --uncompressed Output uncompressed BAM files
FIRE-Filter:
--fire-filter
Convenience: apply the FIRE peak-calling pipeline's fiber-level filters (`--skip-no-m6a`,
`--min-msp 10`, `--min-ave-msp-size 10`). Individual filter flags still override when both
are set. Requires MSP/m6A annotations on the input BAM, so it is a no-op for commands that
run before those annotations exist
--skip-no-m6a[=<SKIP_NO_M6A>]
Drop fibers with no m6A calls. Off by default; `--fire-filter` turns this on unless
explicitly set to `false`. Use `--skip-no-m6a=false` to override when `--fire-filter` is
set [possible values: true, false]
--min-msp <MIN_MSP>
Drop fibers with fewer than `N` MSP calls. Off (0) by default; `--fire-filter` sets this
to 10 unless overridden [env: MIN_MSP=]
--min-ave-msp-size <MIN_AVE_MSP_SIZE>
Drop fibers whose average MSP size is below `N`. Off (0) by default; `--fire-filter` sets
this to 10 unless overridden [env: MIN_AVE_MSP_SIZE=]
Global-Options:
-t, --threads <THREADS> Threads [default: 8]
Debug-Options:
-v, --verbose... Logging level [-v: Info, -vv: Debug, -vvv: Trace]
--quiet Turn off all logging
Make a pileup track of Fiber-seq features from a FIRE bam
Usage: ft pileup [OPTIONS] [BAM]
Arguments:
[BAM] Input BAM file. If no path is provided stdin is used. For m6A prediction, this should be a
HiFi bam file with kinetics data. For other commands, this should be a bam file with m6A
calls [default: -]
Options:
-r, --rgn <RGN> Region string(s) to make a pileup of. e.g. chr1:1-1000 or
chr1:1-1,000 Can be specified multiple times for multiple
regions. If not provided will make a pileup of the whole genome
-b, --bed <BED> BED file with regions to query. If the BED file has a name column
(4th column), the name will be added to each output line for that
region
-o, --out <OUT> Output file [default: -]
-m, --m6a include m6A calls
-c, --cpg include 5mC calls
--haps For each column add two new columns with the hap1 and hap2
specific data
-k, --keep-zeros Keep zero coverage regions
-p, --per-base Write output one base at a time even if the values do not change
--fiber-coverage Calculate coverage starting from the first MSP/NUC to the last
MSP/NUC position instead of the complete span of the read
alignment
--shuffle <SHUFFLE> Shuffle the fiber-seq data according to a bed file of the
shuffled positions of the fiber-seq data
--rolling-max <ROLLING_MAX> Output a rolling max of the score column over X bases
--no-msp No MSP columns
--no-nuc No NUC columns
-h, --help Print help (see more with '--help')
-V, --version Print version
BAM-Options:
-F, --filter <BIT_FLAG> BAM bit flags to filter on, equivalent to `-F` in samtools view
Defaults to 0 (no filtering)
-x, --ftx <FILTER_EXPRESSION> Filtering expression to use for filtering records Example: filter
to nucleosomes with lengths greater than 150 bp -x "len(nuc)>150"
Example: filter to msps with lengths between 30 and 49 bp -x
"len(msp)=30:50" Example: combine 2+ filter expressions -x
"len(nuc)<150,len(msp)=30:50" Filtering expressions support len()
and qual() functions over msp, nuc, m6a, cpg
--ml <MIN_ML_SCORE> Minium score in the ML tag to use or include in the output [env:
FT_MIN_ML_SCORE=] [default: 125]
-u, --uncompressed Output uncompressed BAM files
FIRE-Filter:
--fire-filter
Convenience: apply the FIRE peak-calling pipeline's fiber-level filters (`--skip-no-m6a`,
`--min-msp 10`, `--min-ave-msp-size 10`). Individual filter flags still override when both
are set. Requires MSP/m6A annotations on the input BAM, so it is a no-op for commands that
run before those annotations exist
--skip-no-m6a[=<SKIP_NO_M6A>]
Drop fibers with no m6A calls. Off by default; `--fire-filter` turns this on unless
explicitly set to `false`. Use `--skip-no-m6a=false` to override when `--fire-filter` is
set [possible values: true, false]
--min-msp <MIN_MSP>
Drop fibers with fewer than `N` MSP calls. Off (0) by default; `--fire-filter` sets this
to 10 unless overridden [env: MIN_MSP=]
--min-ave-msp-size <MIN_AVE_MSP_SIZE>
Drop fibers whose average MSP size is below `N`. Off (0) by default; `--fire-filter` sets
this to 10 unless overridden [env: MIN_AVE_MSP_SIZE=]
Global-Options:
-t, --threads <THREADS> Threads [default: 8]
Debug-Options:
-v, --verbose... Logging level [-v: Info, -vv: Debug, -vvv: Trace]
--quiet Turn off all logging
Remove HiFi kinetics tags from the input bam file
Usage: ft clear-kinetics [OPTIONS] [BAM] [OUT]
Arguments:
[BAM] Input BAM file. If no path is provided stdin is used. For m6A prediction, this should be a
HiFi bam file with kinetics data. For other commands, this should be a bam file with m6A
calls [default: -]
[OUT] Output bam file without hifi kinetics [default: -]
Options:
-h, --help Print help
-V, --version Print version
BAM-Options:
-F, --filter <BIT_FLAG> BAM bit flags to filter on, equivalent to `-F` in samtools view
Defaults to 0 (no filtering)
-x, --ftx <FILTER_EXPRESSION> Filtering expression to use for filtering records Example: filter
to nucleosomes with lengths greater than 150 bp -x "len(nuc)>150"
Example: filter to msps with lengths between 30 and 49 bp -x
"len(msp)=30:50" Example: combine 2+ filter expressions -x
"len(nuc)<150,len(msp)=30:50" Filtering expressions support len()
and qual() functions over msp, nuc, m6a, cpg
--ml <MIN_ML_SCORE> Minium score in the ML tag to use or include in the output [env:
FT_MIN_ML_SCORE=] [default: 125]
-u, --uncompressed Output uncompressed BAM files
FIRE-Filter:
--fire-filter
Convenience: apply the FIRE peak-calling pipeline's fiber-level filters (`--skip-no-m6a`,
`--min-msp 10`, `--min-ave-msp-size 10`). Individual filter flags still override when both
are set. Requires MSP/m6A annotations on the input BAM, so it is a no-op for commands that
run before those annotations exist
--skip-no-m6a[=<SKIP_NO_M6A>]
Drop fibers with no m6A calls. Off by default; `--fire-filter` turns this on unless
explicitly set to `false`. Use `--skip-no-m6a=false` to override when `--fire-filter` is
set [possible values: true, false]
--min-msp <MIN_MSP>
Drop fibers with fewer than `N` MSP calls. Off (0) by default; `--fire-filter` sets this
to 10 unless overridden [env: MIN_MSP=]
--min-ave-msp-size <MIN_AVE_MSP_SIZE>
Drop fibers whose average MSP size is below `N`. Off (0) by default; `--fire-filter` sets
this to 10 unless overridden [env: MIN_AVE_MSP_SIZE=]
Global-Options:
-t, --threads <THREADS> Threads [default: 8]
Debug-Options:
-v, --verbose... Logging level [-v: Info, -vv: Debug, -vvv: Trace]
--quiet Turn off all logging
Strip out select base modifications
Usage: ft strip-basemods [OPTIONS] [BAM] [OUT]
Arguments:
[BAM] Input BAM file. If no path is provided stdin is used. For m6A prediction, this should be a
HiFi bam file with kinetics data. For other commands, this should be a bam file with m6A
calls [default: -]
[OUT] Output bam file [default: -]
Options:
-b, --basemod <BASEMOD> base modification to strip out of the bam file [possible values: m6A,
6mA, 5mC, CpG]
--ml-m6a <ML_M6A> filter out m6A modifications with less than this ML value [default: 0]
--ml-5mc <ML_5MC> filter out 5mC modifications with less than this ML value [default: 0]
--drop-forward Drop forward strand of base modifications
--drop-reverse Drop reverse strand of base modifications
-h, --help Print help
-V, --version Print version
BAM-Options:
-F, --filter <BIT_FLAG> BAM bit flags to filter on, equivalent to `-F` in samtools view
Defaults to 0 (no filtering)
-x, --ftx <FILTER_EXPRESSION> Filtering expression to use for filtering records Example: filter
to nucleosomes with lengths greater than 150 bp -x "len(nuc)>150"
Example: filter to msps with lengths between 30 and 49 bp -x
"len(msp)=30:50" Example: combine 2+ filter expressions -x
"len(nuc)<150,len(msp)=30:50" Filtering expressions support len()
and qual() functions over msp, nuc, m6a, cpg
--ml <MIN_ML_SCORE> Minium score in the ML tag to use or include in the output [env:
FT_MIN_ML_SCORE=] [default: 125]
-u, --uncompressed Output uncompressed BAM files
FIRE-Filter:
--fire-filter
Convenience: apply the FIRE peak-calling pipeline's fiber-level filters (`--skip-no-m6a`,
`--min-msp 10`, `--min-ave-msp-size 10`). Individual filter flags still override when both
are set. Requires MSP/m6A annotations on the input BAM, so it is a no-op for commands that
run before those annotations exist
--skip-no-m6a[=<SKIP_NO_M6A>]
Drop fibers with no m6A calls. Off by default; `--fire-filter` turns this on unless
explicitly set to `false`. Use `--skip-no-m6a=false` to override when `--fire-filter` is
set [possible values: true, false]
--min-msp <MIN_MSP>
Drop fibers with fewer than `N` MSP calls. Off (0) by default; `--fire-filter` sets this
to 10 unless overridden [env: MIN_MSP=]
--min-ave-msp-size <MIN_AVE_MSP_SIZE>
Drop fibers whose average MSP size is below `N`. Off (0) by default; `--fire-filter` sets
this to 10 unless overridden [env: MIN_AVE_MSP_SIZE=]
Global-Options:
-t, --threads <THREADS> Threads [default: 8]
Debug-Options:
-v, --verbose... Logging level [-v: Info, -vv: Debug, -vvv: Trace]
--quiet Turn off all logging
Validate a Fiber-seq BAM file for m6A, nucleosome, and optionally FIRE calls
Usage: ft validate [OPTIONS] [BAM]
Arguments:
[BAM] Input BAM file. If no path is provided stdin is used. For m6A prediction, this should be a
HiFi bam file with kinetics data. For other commands, this should be a bam file with m6A
calls [default: -]
Options:
-r, --reads <READS> Number of reads to validate [default: 5000]
-m, --m6a <M6A> The fraction of reads that must have m6A calls to pass validation
[default: 0.5]
-n, --nuc <NUC> The fraction of reads that must have nucleosome and MSP calls to pass
validation [default: 0.5]
-f, --fire Check for FIRE calls in the reads, there must be at least one FIRE call
to pass validation
-a, --aligned <ALIGNED> Check for the fraction of reads with alignment to a reference genome
[default: 0.0]
-p, --phased <PHASED> Check for the fraction of reads with phasing information [default: 0.0]
-k, --kinetics <KINETICS> Check for the fraction of reads with kinetics information [default:
0.0]
-h, --help Print help
-V, --version Print version
BAM-Options:
-F, --filter <BIT_FLAG> BAM bit flags to filter on, equivalent to `-F` in samtools view
Defaults to 0 (no filtering)
-x, --ftx <FILTER_EXPRESSION> Filtering expression to use for filtering records Example: filter
to nucleosomes with lengths greater than 150 bp -x "len(nuc)>150"
Example: filter to msps with lengths between 30 and 49 bp -x
"len(msp)=30:50" Example: combine 2+ filter expressions -x
"len(nuc)<150,len(msp)=30:50" Filtering expressions support len()
and qual() functions over msp, nuc, m6a, cpg
--ml <MIN_ML_SCORE> Minium score in the ML tag to use or include in the output [env:
FT_MIN_ML_SCORE=] [default: 125]
-u, --uncompressed Output uncompressed BAM files
FIRE-Filter:
--fire-filter
Convenience: apply the FIRE peak-calling pipeline's fiber-level filters (`--skip-no-m6a`,
`--min-msp 10`, `--min-ave-msp-size 10`). Individual filter flags still override when both
are set. Requires MSP/m6A annotations on the input BAM, so it is a no-op for commands that
run before those annotations exist
--skip-no-m6a[=<SKIP_NO_M6A>]
Drop fibers with no m6A calls. Off by default; `--fire-filter` turns this on unless
explicitly set to `false`. Use `--skip-no-m6a=false` to override when `--fire-filter` is
set [possible values: true, false]
--min-msp <MIN_MSP>
Drop fibers with fewer than `N` MSP calls. Off (0) by default; `--fire-filter` sets this
to 10 unless overridden [env: MIN_MSP=]
--min-ave-msp-size <MIN_AVE_MSP_SIZE>
Drop fibers whose average MSP size is below `N`. Off (0) by default; `--fire-filter` sets
this to 10 unless overridden [env: MIN_AVE_MSP_SIZE=]
Global-Options:
-t, --threads <THREADS> Threads [default: 8]
Debug-Options:
-v, --verbose... Logging level [-v: Info, -vv: Debug, -vvv: Trace]
--quiet Turn off all logging
Call FIRE peaks using FDR-based peak calling on pileup data
Usage: ft call-peaks [OPTIONS] [BAM]
Arguments:
[BAM] Input BAM file. If no path is provided stdin is used. For m6A prediction, this should be a
HiFi bam file with kinetics data. For other commands, this should be a bam file with m6A
calls [default: -]
Options:
-s, --shuffled <SHUFFLED>
BED file with shuffled fiber positions (from bedtools shuffle) If not provided, will use
all positions as real data (no FDR calculation)
-o, --out <OUT>
Output BED file with called peaks [default: -]
--max-cov <MAX_COV>
Maximum coverage threshold for filtering (optional)
--min-cov <MIN_COV>
Minimum coverage threshold for filtering (optional)
--sd-cov <SD_COV>
Number of standard deviations from median coverage to use for filtering (default: 5) If
set, will calculate median +/- (sd_cov * std_dev) and use those as min/max coverage This
overrides --max-cov and --min-cov if those are not explicitly set [default: 5.0]
--max-fdr <MAX_FDR>
Maximum FDR threshold for peak calling (ignored if --min-fire-frac is set) [default: 0.05]
--min-fire-frac <MIN_FIRE_FRAC>
Minimum fraction of fibers with FIREs required to call a peak If set, skips FDR
calculation and uses this threshold instead For example, 0.5 means at least 50% of fibers
must have a FIRE at the peak position
--min-fire-frac-filter <MIN_FIRE_FRAC_FILTER>
Minimum fraction of fibers with FIREs required as an additional filter (applied WITH FDR)
Unlike --min-fire-frac, this is applied in addition to FDR filtering, not instead of it
For example, 0.3 means at least 30% of fibers must have a FIRE AND FDR must be <= max_fdr
[default: 0.1]
--window-size <WINDOW_SIZE>
Rolling window size for finding local maxima (in base pairs) [default: 200]
--min-frac-overlap <MIN_FRAC_OVERLAP>
Minimum fraction of overlapping FIRE elements for merging peaks (Phase 2) [default: 0.5]
--min-reciprocal-overlap <MIN_RECIPROCAL_OVERLAP>
Minimum reciprocal overlap for merging peaks (Phase 3) [default: 0.75]
--high-reciprocal-overlap <HIGH_RECIPROCAL_OVERLAP>
High reciprocal overlap threshold for initial merging (Phase 1) [default: 0.90]
--max-grouping-iterations <MAX_GROUPING_ITERATIONS>
Maximum number of grouping iterations for merging [default: 10]
--fdr-table <FDR_TABLE>
Skip the FDR table generation and use existing table
--fdr-table-out <FDR_TABLE_OUT>
Output the FDR table to this file
--include-nuc-msp
Include nucleosome and MSP coverage in pileup (default: only FIRE coverage)
--haps
Include haplotype-specific calls
-h, --help
Print help
-V, --version
Print version
BAM-Options:
-F, --filter <BIT_FLAG> BAM bit flags to filter on, equivalent to `-F` in samtools view
Defaults to 0 (no filtering)
-x, --ftx <FILTER_EXPRESSION> Filtering expression to use for filtering records Example: filter
to nucleosomes with lengths greater than 150 bp -x "len(nuc)>150"
Example: filter to msps with lengths between 30 and 49 bp -x
"len(msp)=30:50" Example: combine 2+ filter expressions -x
"len(nuc)<150,len(msp)=30:50" Filtering expressions support len()
and qual() functions over msp, nuc, m6a, cpg
--ml <MIN_ML_SCORE> Minium score in the ML tag to use or include in the output [env:
FT_MIN_ML_SCORE=] [default: 125]
-u, --uncompressed Output uncompressed BAM files
FIRE-Filter:
--fire-filter
Convenience: apply the FIRE peak-calling pipeline's fiber-level filters (`--skip-no-m6a`,
`--min-msp 10`, `--min-ave-msp-size 10`). Individual filter flags still override when both
are set. Requires MSP/m6A annotations on the input BAM, so it is a no-op for commands that
run before those annotations exist
--skip-no-m6a[=<SKIP_NO_M6A>]
Drop fibers with no m6A calls. Off by default; `--fire-filter` turns this on unless
explicitly set to `false`. Use `--skip-no-m6a=false` to override when `--fire-filter` is
set [possible values: true, false]
--min-msp <MIN_MSP>
Drop fibers with fewer than `N` MSP calls. Off (0) by default; `--fire-filter` sets this
to 10 unless overridden [env: MIN_MSP=]
--min-ave-msp-size <MIN_AVE_MSP_SIZE>
Drop fibers whose average MSP size is below `N`. Off (0) by default; `--fire-filter` sets
this to 10 unless overridden [env: MIN_AVE_MSP_SIZE=]
Global-Options:
-t, --threads <THREADS> Threads [default: 8]
Debug-Options:
-v, --verbose... Logging level [-v: Info, -vv: Debug, -vvv: Trace]
--quiet Turn off all logging