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Forum: Bioinformatics 09-06-2012, 09:06 AM
Replies: 0
Views: 1,694
Posted By jfk
Sliding window/genome coverage from pileup files?

I have SOLiD whole genome sequence data from different yeast strains (S. cerevisiae) that have been processed using samtools.

I have used samtools pileup and have .pileup file for all my yeast...
Forum: Bioinformatics 05-02-2012, 06:57 AM
Replies: 1
Views: 1,164
Posted By jfk
Problem solved. The windows carriage return...

Problem solved.

The windows carriage return creeping into my script... was using notepad++ on my linux desktop.

.. lesson: use vim/gedit!
Forum: Bioinformatics 05-02-2012, 12:10 AM
Replies: 1
Views: 1,164
Posted By jfk
Bfast match .bmf? file - anybody seen .bmf? before

Hi everyone

I've used BFAST (0.7.0a) before on our institute computing cluster successfully before, however, after running 'bfast match' last night I have a '.bmf?' file instead of the normal...
Forum: Bioinformatics 02-27-2012, 03:26 PM
Replies: 13
Views: 4,685
Posted By jfk
I would be interested in generating a consensus...

I would be interested in generating a consensus sequence - can mpileup do this as I'm not sure from the documentation that this is possible?

mpileup is fine for variant calling and SNP detection -...
Forum: Bioinformatics 02-27-2012, 09:57 AM
Replies: 13
Views: 4,685
Posted By jfk
I ran into this problem too as the local cluster...

I ran into this problem too as the local cluster installation of samtools is v 0.1.18. The work I am repeating/checking requires pileup and the ability to generate a consensus sequence.

Locally I...
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