Hi all,
I have data from a miseq run in three gzipped fastq files: R1, R2, and the index file (I1). I also have a mapping file with barcode sequences.
I need to demultiplex these files and am trying to figure out how to do this without merging reads. In the end, I need one R1 and one R2 file with the fastq sequences for each sample.
I was looking at split_libraries_fastq.py:
Demultiplex and quality filter (at Phred >= Q20) two lanes of Illumina fastq data and write results to ./slout_q20.:
split_libraries_fastq.py -i lane1_read1.fastq.gz,lane2_read1.fastq.gz -b lane1_barcode.fastq.gz,lane2_barcode.fastq.gz --rev_comp_mapping_barcodes -o slout_q20/ -m map.txt,map.txt --store_qual_scores -q 19
But I don't have two mapping files, so I'm assuming this might not be the best approach.
Thanks for any advice you might have!
Cheers,
~Lina