GetrRNAStatistics: Get the total number of rRNA read counts from bam file....

In njmadrid/RNAseqQuality: Provides a set of functions for summarizing the quality of RNA-seq data.

Description

Note that samtools idxstats may or may not include secondary alignments. This will depend on how the reads were aligned. See the documention for samtools idxstats and the aligner used to create the bam file. The bam file must have been aligned to a reference genome containing chromosone GL000220.1 total reads mapping to GL0000220.1 or know rRNA regions defined by Ensembl

Usage

GetrRNAStatistics(BamFilePath)

Arguments

BamFilePath

location of aligned bam file. Corresponding bai index file must be in the same directory.

Value

An integer for the total number of rRNA read counts in a given bam file.

Author(s)

Nathaniel J. Madrid, Jason Byars

Examples

BamFilePaths <- dir(path="/home/ubuntu/Projects/RNAseqPackage/bams", pattern=".*.bam$", full.names=T)
# samtools idxstats must be installed on the local system.
# Note that samtools idxstats may or may not include secondary alignments. This will depend on how the reads
# were aligned. See the documention for samtools idxstats and the aligner used to create the bam file.
rRNAStatsDF = GetrRNAStatistics(BamFilePaths[1])

njmadrid/RNAseqQuality documentation built on May 20, 2019, 3:32 p.m.