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Old 02-26-2015, 07:12 AM   #11
Location: USA

Join Date: Sep 2014
Posts: 18
Default BBSplit: limit amount of ref

Hi Brian,

I tried BBSplit with four ref files without any success. Is there any limit to the number of ref files?

java -Xmx29g -cp /path/to/current align2.BBSplitter in1=clean_ecc_100_r1.fastq.gz in2=clean_ecc_100_r2.fastq.gz ref=/path/to/resources/ref1.fasta,/path/to/resources/ref2.fasta,/path/to/resources/ref3.fasta,/path/to/resources/ref4.fasta basename=out_%.fastq.gz out1=unmapped_r1.fastq.gz out2=unmapped_r2.fastq.gz ambig2=split

However it work fine with 3 ref files. I tried with interactions of various group of 3 ref files with success.

P.S. When do you think is better to perform BBSplit after or before ecc/quality trim?

Thanks again

Last edited by vingomez; 02-26-2015 at 07:29 AM. Reason: Add a question
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