buildSpliceJunctionFiles: Build Splice Junction Index and Maps

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

Build Splice Junction Index and Maps

Description

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

Usage

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 March 24, 2024, 4:16 p.m.