filter_bam: BAM file filter

In stiv1n/CYCLeR: CircRNA transcriptome assembly tool

BAM file filter

Description

A wrapper function for samtools use to trim the files

Usage

filter_bam(BSJ_gr, sample_table, samtools_prefix)

Arguments

BSJ_gr	a GRange of BSJ cooredinates
sample_table	sample table formatted according to the manual, Must contain “sample_name” “treatment” “file_bam” “lib_size” “read_len”; NB the values in column “treatment” can only be “control” and “enriched”
samtools_prefix	a string that corresponds to user's samtools run prefix

Details

This function removes the BAM file reads that do not overlap with the BSJ loci. This significantly speeds us the feature detection and lowers the virtual memory requirements

Value

BAMFileList object with info on the trimmed files

Author(s)

Stefan Stefanov

stiv1n/CYCLeR documentation built on Sept. 15, 2022, 4:39 p.m.