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dan 09-18-2012 09:08 AM

Challenging read mapping problem

I have about 70Gbp of paired-end data from potato [1] that I'd like to map to one of the chromosomes (chr04). I only want pairs where one end or the other, or both, matches chr04.

Aside from the scale of the problem, the format of the files is a pain, because each pair is in a different file.

Any tips on how to do this (efficiently)?

A prize goes to the best answer ;-)



TiborNagy 09-20-2012 05:00 AM

Most of the aligners handle paired data in different files. I do not think it is a problem. Use BWA or other aligner program.

dan 09-20-2012 05:47 AM

Yup, bowtie worked fine.

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