MMalign: Align fastq.gz files with Minimap2

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

Align fastq.gz files with Minimap2

Description

This function is a wrapper for Minimap2 with stringent parameters optimized for ONT/PacBio sequenced data. It performs sam to bam conversion to reduce space, and .bam output is necessary for downstream analysis

Usage

MMalign('FastqFiles/','~/minimap2',
'~/mm10.fa',32)

Arguments

fqFolder	fastq.gz files from a single sample or replicate, or barcoded output
mmProgPath	path to Minimap2 aligner
refGenome	path to reference genome.fa
numThreads	number of parallel threads to use, Defaults to 8

Value

MMoutput folder containing minimap2 aligned files and report

See Also

MapAndFilter

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