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/