This tool takes an alignment file in SAM or BAM format and feature file in GFF format and calculates the number of reads mapping to each feature. It uses the htseq-count script that is part of the HTSeq python module
htseq-count [options] sam_file gff_file
-h, --help show this help message and exit
-m MODE, --mode=MODE
mode to handle reads overlapping more than one feature(choices: union, intersection-strict, intersection-nonempty; default: union)
-s STRANDED, --stranded=STRANDED
whether the data is from a strand-specific assay. Specify 'yes', 'no', or 'reverse' (default: yes). 'reverse' means 'yes' with reversed strand interpretation
-a MINAQUAL, --minaqual=MINAQUAL
skip all reads with alignment quality lower than the given minimum value (default: 0)
-t FEATURETYPE, --type=FEATURETYPE
feature type (3rd column in GFF file) to be used, all features of other type are ignored (default, suitable for Ensembl GTF files: exon)
-i IDATTR, --idattr=IDATTR
GFF attribute to be used as feature ID (default, suitable for Ensembl GTF files: gene_id)
-o SAMOUT, --samout=SAMOUT
write out all SAM alignment records into an output SAM file called SAMOUT, annotating each line with its feature assignment (as an optional field with tag 'XF')
-q, --quiet suppress progress report and warningsa