process_qseq.rst

process_qseq.py

process_qseq.py -- Given a directory of per-swath qseq files, this script generates a single fastq per lane.

Description:

Usage: process_qseq.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_dir

The input directory

-o, --output_dir

The output directory

-r, --read

The read number to consider

[OPTIONAL]

-l, --lanes

The lane numbers to consider, comma-separated [defaut: 1,2,3,4,5,6,7,8]

-b, --bases

The number of bases to include (useful for slicing a barcode) [defaut: all]

--ignore_pass_filter

Ignore the illumina pass filter [default:False; reads with 0 in pass filter field are discarded]

Output:

Generate fastq files from all lanes of read 1 data in the current directory.

process_qseq.py -i ./ -o ./fastq/ -r 1

Generate fastq files from all lanes of read 2 data in the current directory, truncating the sequences after the first 12 bases.

process_qseq.py -i ./ -o ./fastq/ -r 2 -b 12