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Old 03-02-2018, 05:47 AM   #5
Location: South Africa

Join Date: Sep 2013
Posts: 12
Smile worked finally - but had to increase kmer and literal..


Thank you, I finally got it to work with literal, but I had to increase the length of the literal to 20 X T and increase the kmer to 25. With literal=TTTTTTTT k=5 I got 98% of the reads filtered out, even with mm=false and hdist=0...

Ok, another question - how can I use bbduk to split my file into multiple files based on a inline barcode of 8 bp at the 5' end?

I have 100 bp SE end reads and they are multiplexed using a 32 X 8 base barcodes. I have used sabre before but it is on another machine and I would like to avoid transferring files between different servers if possible.

DrYak is offline   Reply With Quote