HTSeqGenie (version 4.2.0)

countGenomicFeaturesChunk: Count reads by genomic Feature

Description

Count reads by genomic Feature

Usage

countGenomicFeaturesChunk(save_dir, genomic_features)

Arguments

save_dir

PAth to a pipeline run's save dir

genomic_features

A list of genomic features to tally

Value

Nothing

Details

given a BAM-file output from gsnap (with the MD tag), count hits to exons, genes, ncRNAs, etc. and quantify miRNA/ncRNA contaminatino