alignReadsChunk: Genomic alignment

Description Usage Arguments Details Value

View source: R/alignReads.R

Description

Genomic alignment using gsnap.

Usage

1
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

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.

Value

List of alignment files in BAM format


HTSeqGenie documentation built on Nov. 8, 2020, 6:12 p.m.