Challenging read mapping problem

[dan]

Hi,

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 ;-)


Cheers,
Dan.

[1] http://www.ebi.ac.uk/ena/data/view/SRA029323

[TiborNagy]

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]

Yup, bowtie worked fine.