Last data update: 2014.03.03

 R: Genomic alignment
alignReadsChunkR Documentation

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

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

Results


Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO