remove_contam_reads: Remove contaminating reads in a parallel fashion.

In shahlab/RiboRet: Shah lab RiboRet functions

Description

This function removes contaminating reads, generally rRNA/tRNA reads, but can be configured to remove reads mapping to wherever the user chooses. It uses a user provided GFF to remove reads that map to user designated regions.

Usage

remove_contam_reads(bamList, gffLoc, contaminants)

Arguments

bamList	A named list of bam files
gffLoc	The path to a gff
contaminants	A character vector containing the thing in gffCol you want to remove, for example, rRNA. This is searched for in the gff "type" column to make a gff that defines the contaminating reads. This is currently not flexible because it requires a "type" column.

Value

A list of bams depleted of contaminating reads

shahlab/RiboRet documentation built on Dec. 23, 2021, 1:17 a.m.