2 enzyme GBS UNEAK trickery

Want to run UNEAK on a bunch of samples that you sequenced using 2 enzyme GBS? You came to the right place!

This takes R1.fastq.gz and R2.fastq.gz files and makes a single file containing both reads with the appropriate barcodes put on read 2 and the CGG RE site changed to the Pst sequence. This lets you use all of your data in UNEAK… well at least the first 64 bases of all your data!

This also deals with the fact that we get data that is from one lane but split into many files. See example LaneInfo file*. You will also need an appropriately formatted UNEAK key file.

*Only list READ1 in this file. It will only work if your files are named /dir/dir/dir/ABC_R1.fastq.gz and /dir/dir/dir/ABC_R2.fastq.gz.

so the file would read:
/dir/dir/dir/ ABC_R1.fastq C5CDUACXX 3

This is also made to work with .gz fastq files.

greg@computer$ perl bin/MultiLane_UneakTricker.pl design/UNEAK_KEY_FILE design/LaneInfo.txt /home/greg/project/UNEAK/Illumina

You must have the GBS_Fastq_BarcodeAdder_2Enzyme.pl* in the same bin folder. You also need to make a “tmp” folder.


protip: UNEAK will be fooled by soft links so you can use them instead of copying your data.