The Fiber-seq BAM format

The Fiber-seq BAM format adds to m6A BAM data from a PacBio (ft predict-m6a) or ONT (dorado) sequencing run with m6A.

The following tags are added to the BAM file:

• ns:B:I,: Nucleosome start sites (0-based) on the forward strand of the sequencing read (u32).
• nl:B:I,: Equal length array to ns of nucleosome lengths (u32).
• as:B:I,: MSP start sites (0-based) on the forward strand of the sequencing read (u32).
• al:B:I,: Equal length array to as of MSP lengths (u32).
• aq:B:C,: Quality scores for the MSP [0, 255] (u8). This tag is optional and added by ft fire.

The ns or as tag do not need to begin or end at the start or end of the read; however, once begun, they must be contiguous. i.e. the ns and as tags must combine to form a contiguous set of alternating nucleosome and MSP sites. The ns, nl, as, and al tags are added to the BAM file automatically using ft predict-m6a or later using the ft add-nucleosomes command.

The aq tag is added using the ft fire command and represents the estimated precision of the MSP being a FIRE. Specifically, the estimated precision of a FIRE is the value of the aq tag divided by 255.