FPKM_count.py¶

Calculate raw read count, FPM (fragments per million), and FPKM (fragments per million mapped reads per kilobase exon) for each gene in a BED file.

Usage¶

FPKM_count.py -i input.bam -r gene_model.bed -o output_prefix

Option	Description	Default
`-i`, `--input-file`	Alignment file in BAM format (SAM not supported)	Required
`-o`, `--out-prefix`	Prefix of output files	Required
`-r`, `--refgene`	Reference gene model in BED format	Required
`-d`, `--strand`	Strand rule: `1++,1--,2+-,2-+` or `1+-,1-+,2++,2--` or `none`	None
`-u`, `--skip-multi-hits`	Skip multi-hit reads	Off
`-e`, `--only-exonic`	Only count reads falling within exons	Off
`-q`, `--mapq`	Minimum mapping quality for "uniquely mapped"	30
`-s`, `--single-read`	Weight for read pairs with only one end mapped (0–1)	1

Tab-separated file with columns: chrom, start, end, name, score, strand, raw_count, FPM, FPKM.