inner_distance.py¶

Calculate the inner distance (insert size) between read pairs for paired-end RNA-seq data. The inner distance is the gap between the end of read 1 and the start of read 2 on the transcript.

Usage¶

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

Options¶

Option	Description	Default
`-i`, `--input-file`	Alignment file in BAM or SAM format	Required
`-o`, `--out-prefix`	Prefix of output files	Required
`-r`, `--refgene`	Reference gene model in BED format	Required
`-k`, `--sample-size`	Number of read pairs to use	1000000
`-l`, `--lower-bound`	Lower bound of inner distance (bp)	-250
`-u`, `--upper-bound`	Upper bound of inner distance (bp)	250
`-s`, `--step`	Step size (bp) for histogram	5
`-q`, `--mapq`	Minimum mapping quality for "uniquely mapped"	30

Output¶

prefix.inner_distance.txt — inner distances per read pair
prefix.inner_distance_freq.txt — inner distance histogram
prefix.inner_distance_plot.r — R script for histogram
prefix.inner_distance_plot.pdf — inner distance histogram (if R is available)

Tip

Negative inner distances indicate overlapping read pairs, which is common for short fragments.