View Single Post
Old 01-05-2017, 01:57 PM   #405
Brian Bushnell
Super Moderator
 
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
Default

I'm not really sure what the problem is in this case. Tadpole really doesn't care what the input reads look like, whether they are paired, or what format they are in. Can you post the complete error message?

What you are planning to do should work fine. On the command line, it would be something like this:

Code:
bbmap.sh ref=ref.fa in=reads.fq outm=mapped.fq outu=junk.fq
tadpole.sh in=mapped.fq out=contigs.fa k=62
I'm not sure how that would translate to Geneious. Note, by the way, that you can remove homopolymer reads with BBDuk like this:

Code:
bbduk.sh in=reads.fq out=filtered.fq entropy=0.01
That will remove polymonomer reads only (AAAA...). At entropy=0.19 it will also remove polydimer reads (ACACAC...). At entropy=0.29 it will remove polytrimers (ACTACT...), and at 0.34 it will remove polytetramers. E.coli reads seem to have an average entropy of around 0.985 by my calculation method.
Brian Bushnell is offline   Reply With Quote