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Forum: Ion Torrent 11-16-2015, 12:56 PM
Replies: 5
Views: 3,013
Posted By Brian Bushnell
Map to the reference with BBMap, like this: ...

Map to the reference with BBMap, like this:

bbmap.sh ref=reference.fa in=reads.fq out=mapped.sam mhist=mhist.txt ehist=ehist.txt qhist=qhist.txt indelhist=indelhist.txt

BBMap will print useful...
Forum: Ion Torrent 11-16-2015, 12:31 PM
Replies: 5
Views: 3,013
Posted By Brian Bushnell
You shouldn't error-correct if you are looking...

You shouldn't error-correct if you are looking for rare variants (much less than the 50% ratio of a normal heterozygous diploid variant), or are doing amplicon sequencing, or are looking at tumor...
Forum: Ion Torrent 11-16-2015, 12:01 PM
Replies: 5
Views: 3,013
Posted By Brian Bushnell
There's no problem with error-correcting data...

There's no problem with error-correcting data multiple times. But if you error-correct it, be sure to use a program that can tolerate indel-type errors.
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