HTSeqGenie (version 4.2.0)

alignReadsChunk: Genomic alignment

Description

Genomic alignment using gsnap.

Usage

alignReadsChunk(fp1, fp2 = NULL, save_dir = NULL)

Arguments

fp1

Path to FastQ file

fp2

Path to second FastQ file if paired end data, NULL if single ended

save_dir

Save directory

Value

List of alignment files in BAM format

Details

Aligns reads in fp1 and fp2 to genome specified via global config variable alignReads.genome. Gsnap output is converted into BAM files and sorted + indexed.