buildRiboClearingFiles: Build Ribo Clearing Index and Map

Description Usage Arguments Details Value Note Author(s)

Description

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

Usage

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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 Dec. 7, 2018, 8:01 a.m.