buildSpliceJunctionFiles: Build Splice Junction Index and Maps

Description Usage Arguments Details Value Note Author(s)

Description

Create the Bowtie Index and maps for the Splice Junctions portion of the alignment pipeline.

Usage

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buildSpliceJunctionFiles(speciesID, genomicFastaFile, 
	outPath = ".", spliceMapPrefix = "spliceMap", 
	fragmentSize = 60, maxExonSkip = 2, intronSplicesToo = TRUE, 
	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 SpliceJunction map files

spliceMapPrefix

a character string prefix for each created map file

fragmentSize

the number of bases in each exon end fragment, to become half of each splice junction entry in the index. Typically about 90% of the length of a typical raw read.

maxExonSkip

maximum number of skipped exons, to add exon skipping splice junctions to the index

intronSplicesToo

logical, should intron-exon and intron-intron alternate splices also be added to the index

Details

The Splice Junction index is composed of lots of tiny sequences that represent the standard and alternative splicing of exons, as defined by the ExonMap. Each sequence extends fragmentSize bases into each of the two exons(introns) being joined.

Value

a Splice Junction Bowtie index and a splice map for each SeqID (chromosome) 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. 14, 2018, 3:04 p.m.