FASDA-ABUNDANCE(1)

NAME

fasda abundance - Compute abundances from SAM data

SYNOPSIS

fasda abundance features.gff3 alignment-file [alignment-file ...]

DESCRIPTION
fasda abundance computes raw read counts from one or more SAM/BAM/CRAM files overlapping each features in a GFF3 file. Output is an abundance.tsv file in the same format as those produced by kallisto. Abundances in the output are raw counts of properly paired reads that are not flagged as secondary alignments, failed QC, duplicate, or supplementary. For paired-end reads, both mates are counted separately, so the counts should be expected to reflect about double the number of fragments aligned. Any normalization of counts is left to downstream tools such as fasda-normalize(1).

FILES
features.gff3
alignment.bam

SEE ALSO
fasda-normalize(1), fasda-fold-change(1)

BUGS
Please report bugs to the author and send patches in unified diff format. (man diff for more information)

AUTHOR
J. Bacon