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

Description:

Usage: process_iseq.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_fps

The input filepaths (either iseq or gzipped iseq format; comma-separated if more than one). See Processing Illumina Data tutorial for a description of the iseq file type.

-o, --output_dir

The output directory

-b, --barcode_length

Length of the barcode

[OPTIONAL]

--barcode_in_header

Pass if barcode is in the header index field (rather than at the beginning of the sequence)

--barcode_qual_c

If no barcode quality string is available, score each base with this quality [default: b]

Output:

Generate fastq files from lanes 1 and 2 (read 1 data) where barcodes are contained as the first tweleve bases of the sequences.

process_qseq.py -i ./s_1_1_sequence.txt,./s_2_1_sequence.txt -b 12 -o ./fastq/

Generate fastq files from the gzipped lanes 1 and 2 (read 1 data) where barcodes are contained as the first tweleve bases of the sequences.

process_qseq.py -i ./s_1_1_sequence.txt.gz,./s_2_1_sequence.txt.gz -b 12 -o ./fastq/