ft-center
ft-center
This command centers Fiber-seq data around given reference positions. This is useful for making aggregate m6A and CpG observations, as well as visualization of SVs
Inputs and options
See the help message for details.
Output description
This command writes Fiber-seq data in a tab-delimited format to stdout that has been centered relative to positions specified in the input bed file.
| Column | Description |
|---|---|
| chrom | Chromosome |
| centering_position | The position on the chromosome about which data is being centered. |
| strand | The strand of the centering position. |
| subset_sequence | The sequence of the read around the centering position. |
| reference_start | The start position of the read in the reference. |
| reference_end | The end position of the read in the reference. |
| query_name | The name of the sequencing read |
| RG | The read group the read belongs to |
| centered_query_start | The start position of the read relative to the centering position |
| centered_query_end | The end position of the read relative to the centering position |
| query_length | The length of the read |
Additional columns specific to long (default) format
| Column | Description |
|---|---|
| centered_position_type | The type of position being centered. One of: m6A, 5mC, nuc, msp. |
| centered_start | The start position of the “feature” relative to the centering position |
| centered_end | The end position of the “feature” relative to the centering position |
| centered_quality | The quality of the “feature” relative to the centering position (ML value) |
Additional columns specific to the wide format
| Column | Description |
|---|---|
| centered_m6a_positions | A comma separated list of m6a positions |
| m6a_qual | The quality of the m6a positions (ML value) |
| centered_5mC_positions | A comma separated list of 5mC positions |
| 5mC_qual | The quality of the 5mC positions (ML value) |
| centered_nuc_starts | A comma separated list of nuc starts |
| centered_nuc_ends | A comma separated list of nuc ends |
| centered_msp_starts | A comma separated list of msp starts |
| centered_msp_ends | A comma separated list of msp ends |
| query_sequence | The sequence of the read |
Note if the --wide flag is used with the --reference flag some positions in the comma separated lists can be NA when the reference sequence has an insertion or deletion relative to the read sequence at that position.