feature_count_par: count the number of reads that overlap with genomic features

In pcahan1/CellNet: Assess and improve cell fate engineering with network biology

count the number of reads that overlap with genomic features

Description

count the number of reads that overlap with genomic features uses samtools/htseq-count

Usage

feature_count_par(sampTab, gtfpath, sname = "sra_id", target = "mouse")

Arguments

sampTab	sample table
gtfpath	gtf of genomic features
sname	column to use to name output files
target	species, e.g. 'mouse'

Value

sample table with hit rates appended

pcahan1/CellNet documentation built on May 18, 2023, 4:58 p.m.