MapAndFilter: Extract isoform information from aligned reads

In noush-joglekar/scisorseqr: Processes long reads for differential isoform analysis

Extract isoform information from aligned reads

Description

This function follows the alignment function. It is a wrapper for several scripts that impose checks and balances on the mapping quality, consensus nature of splice sites, and annotated start and end sites per transcript.

Usage

MapAndFilter('LRoutput','gencode.vM21.annotation.gtf.gz',16)

Arguments

outputDir	location within the working directory for files that will be created during this process
annoGZ	annotation.gtf.gz file. Defaults to v21 mm10
numThreads	number of threads for parallel processes. Defaults to 12
seqDir	directory containing chromosome.fa.gz files
filterFullLength	OPTIONAL logical indicating whether reads should be filtered for having start and end sites falling into annotated cage peaks or polyA sites. Defaults to FALSE
cageBed	OPTIONAL bed.gz file containing annotated CAGE peaks
polyABed	OPTIONAL bed.gz file containing annotated polyA sites
cp_distance	OPTIONAL distance from annotated CAGE peak or polyA site for a read to be considered full-length. Defaults to 50
genomeVersion	genome and version for GFF output file. Defaults to mm10
onlyFullLength	OPTIONAL If you have already run this command without annotated CAGE and PolyA sites and now want to just run that portion, set to TRUE. Defaults to FALSE

Value

directory containing several bam, gff.gz, and flat files necessary for downstream analysis

See Also

STARalign MMalign

noush-joglekar/scisorseqr documentation built on March 18, 2023, 8:06 p.m.