Paired End for Stacks and UNEAK

Both stacks and uneak are made for single end reads. If you have paired end data here is a little cheat that puts “fake” barcodes onto the mate pairs and prints them all out to one file. It also adds the corresponding fake quality scores.

perl GBS_fastq_RE-multiplexer_v1.pl BarcodeFile R1.fastq R2.fastq Re-barcoded.fastq

BarcodeFile should look like (same as for my demultiplexing script) spaces must be tabs:
sample1 ATCAC
sample2 TGCT

# note this could also look like this:
ATCAG ATCAG
TGCT TGCT

As it does not actually use the names (it just looks at the second column).

Here it is:
GBS_fastq_RE-multiplexer_v1

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