Usage¶

Basic Command¶

fcount-rs -a <annotation.gtf> -o <output.txt> <bam_files>...

Option	Description
`-a, --annotation <PATH>`	GTF/GFF annotation file
`-o, --output <PATH>`	Output count matrix file
`<BAM_FILES>`	One or more BAM/SAM input files

Option	Description	Default
`-t, --type <TYPE>`	Feature type to count	`exon`
`-g, --gene-id <ATTR>`	GTF attribute for gene ID	`gene_id`
`-f, --feature-level`	Count at feature level instead of gene level	off

Option	Description	Default
`-p, --paired`	Count fragments instead of reads	off
`-B, --both-aligned`	Require both mates aligned	off
`-C, --count-chimeric`	Count chimeric fragments	off
`--min-frag-len <INT>`	Minimum fragment length	50
`--max-frag-len <INT>`	Maximum fragment length	600

Option	Description	Default
`-s, --strand <MODE>`	Strand mode: 0=unstranded, 1=stranded, 2=reversely stranded	0

Option	Description	Default
`-M, --multi-mapping`	Count multi-mapping reads	off
`--fraction`	Use fractional counting	off
`--primary`	Count primary alignments only	off

Option	Description	Default
`-O, --multi-overlap`	Allow reads assigned to multiple features	off
`--min-overlap <INT>`	Minimum overlapping bases	1
`--frac-overlap <FLOAT>`	Minimum fraction of read overlapping feature	0.0
`--frac-overlap-feature <FLOAT>`	Minimum fraction of feature overlapped	0.0
`--largest-overlap`	Assign to feature with largest overlap only	off

Option	Description	Default
`-Q, --min-mapq <INT>`	Minimum mapping quality	0
`--ignore-dup`	Ignore duplicate reads	off

Option	Description	Default
`-T, --threads <INT>`	Number of threads	1

Option	Description
`-R, --details <PATH>`	Output detailed read assignments
`-q, --quiet`	Suppress progress output