SEQanswers - View Single Post - BBDuk java error when filtering using entropy?

DrYak · 03-02-2018, 05:47 AM

Hi,

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.

Cheers,
Dave

03-02-2018, 05:47 AM	#5
DrYak Member Location: South Africa Join Date: Sep 2013 Posts: 12	worked finally - but had to increase kmer and literal.. Hi, 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. Cheers, Dave