BGI had previously supplied us with demultiplexed GBS FASTQ files. However, they had not provided us with the information/data on how those files were created. I contacted them and they’ve given us the two original FASTQ files, as well as the library index file and corresponding script they used for demultiplexing all of the files. The Jupyter (iPython) notebook below updates our checksum and readme files in our server directory that’s hosting the files: http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/
See Jupyter Notebook below for processing details.
Jupyter Notebook: 20160427_Oly_GBS_data_management.ipynb