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Old 06-23-2014, 07:02 PM   #17
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,695
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Olaf,

Currently, BBNorm uses single interleaved files for temporary storage when using multiple passes. And I have not implemented any way to specify dual files in intermediate stages, since everyone at JGI uses interleaved files for everything.

You have two options.
1) You could set "passes=1", which is faster, but I don't recommend it because it doesn't give as good results as 2-pass normalization.
or
2) You could specify only a single output file, which will get interleaved reads:

bbnorm.sh in1=R1.fastq.gz in2=R2.fastq.gz out=R12.bbnorm.fastq.gz prefilter=t tossbadreads=t ecc=t fixspikes=t qin=33 -Xmx72g target=40

...Then, if you need to, de-interleave it afterward:

reformat.sh in=R12.bbnorm.fastq.gz out1=R1.bbnorm.fastq.gz out2=R2.bbnorm.fastq.gz

Sorry for the inconvenience! I'll try to fix that by the next release, though unlike documenting the "qin" flag, this will take more work so no guarantees. Thanks for bringing it to my attention. FYI, the flag "interleaved" has no effect on output, only input.

-Brian

Last edited by Brian Bushnell; 06-23-2014 at 07:05 PM.
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