BBnorm not outputting txt files when trying to determine ploidy on pb fastq.gz reads
Entering edit mode
15 months ago

I'm trying to determine ploidy of my genome using BBnorm. I am not getting any error but no txt files are produced. in=reads.fq khist=khist.txt peaks=peaks.txt

or equivalently in=reads.fq khist=khist.txt peaks=peaks.txt passes=1 prefilter minprob=0 minqual=0 mindepth=0

This is my input: in=A.subreads.fastq.gz khist=khist.txt peaks=peaks.txt

Can it use fastq.gz files? Can you use illumina reads?

kmer khist bbnorm bbmap ploidy • 379 views
Entering edit mode

All BBTools can use compressed files. They can use Illumina data for sure. Title of your post seems to suggest that you may have PacBio data? That may not work since with exception of most BBTools programs are for short read data. That said can you try the following?

For usage indicates : in=<input> hist=<histogram output>

For in=<input> out=<reads to keep> outt=<reads to toss> hist=<histogram output>

I assume you are using commands from BBNorm Guide page.


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