buildRiboClearingFiles: Build Ribo Clearing Index and Map

In robertdouglasmorrison/DuffyNGS: Duffy Lab NGS Analysis Pipeline for RNA-seq, DNA-seq, ChIP-seq, and RIP-seq

Build Ribo Clearing Index and Map

Description

Create the Bowtie Index and map for the RiboClearing portion of the alignment pipeline.

Usage

buildRiboClearingFiles(speciesID, genomicFastaFile, 
	outPath = ".", mapFile = "riboMap.txt", 
	tailSize = 24, verbose = TRUE)

Arguments

speciesID	the SpeciesID for this organism
genomicFastaFile	the file of FASTA sequences, or a folder of FASTA files, for this organism. See getFastaSeqFromFilePath
outPath	destination folder for the created RiboClearing map file
mapFile	name for the newly created RiboClearing map file
tailSize	number of bases to extend beyond the gene edges for constructing the Bowtie index of the genes to be cleared. This allows reads that span the gene boundary to be matched by the index and thus cleared.

Details

Exactly which genes go into the RiboClearing index is determined by the RrnaMap. See MapSets.

Value

a Ribo Clearing Bowtie index and RiboClear map are written to disk

Note

Indexes and maps may need to be moved to the folder of Bowtie indexes.

Author(s)

Bob Morrison

robertdouglasmorrison/DuffyNGS documentation built on March 24, 2024, 4:16 p.m.