RNA_fragment_size.py¶

Calculate fragment size statistics for each gene/transcript. Reports the number of fragments used, plus mean, median, and standard deviation of fragment size.

Usage¶

RNA_fragment_size.py -i input.bam -r gene_model.bed

Options¶

Option	Description	Default
`-i`, `--input`	Input BAM file	Required
`-r`, `--refgene`	Reference gene model in BED format (standard 12-column)	Required
`-q`, `--mapq`	Minimum mapping quality for "uniquely mapped"	30
`-n`, `--frag-num`	Minimum number of fragments per gene	3

Output¶

Tab-separated output to stdout with columns: gene, chrom, start, end, fragment_count, mean_size, median_size, stdev_size.