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read_distribution.py

Calculate how mapped reads are distributed over genomic features: exons, introns, UTRs, intergenic regions, etc.

The following reads are skipped: QC-failed, PCR duplicates, unmapped, non-primary (secondary).

Usage

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

Options

Option Description Default
-i, --input-file Alignment file in BAM or SAM format Required
-r, --refgene Reference gene model in BED format Required

Output

Prints a table to stdout with read counts and tags for each genomic feature:

Group               Total_Tags         Tag_count          Tags/Kb
CDS_Exons           ...                ...                ...
5'UTR_Exons         ...                ...                ...
3'UTR_Exons         ...                ...                ...
Introns             ...                ...                ...
TSS_up_10kb         ...                ...                ...
TES_down_10kb       ...                ...                ...