Post date: May 13, 2015 4:8:27 PM
Many of the IDs were not correct, so I had to fix these mistakes and re-parse the barcodes. Here are the correct numbers from the parse report (this is in /pscratch/A01963476/data/gbsGomp006to008/Parsed/):
Good mids count: 235923391
Bad mids count: 19901625
Number of seqs with potential MSE adapter in seq: 54819449
Seqs that were too short after removing MSE and beyond: 855510
I split the parsed file into individual fastq files for all of the samples, these are ready to be aligned with GATK.