Post date: Mar 04, 2015 7:45:5 PM
I now have the GBS alfalfa data. The data are currently in /pscratch/A01963476/data/gbsGomp006to008/Sequences/, but I might move them. This directory also includes a Martin's data and Zach's scorpion data. The alfalfa data are library gomp008.
I parsed the barcode sequences for these data and here is what I ended up with:
Good mids count: 235618318
Bad mids count: 20206703
Number of seqs with potential MSE adapter in seq: 54819449
Seqs that were too short after removing MSE and beyond: 855510
Note, there appear to be some individual barcodes with small counts, but I will look at this more once I split the data by individual, which is the next step.