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Old 09-18-2012, 09:08 AM   #1
dan
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Default Challenging read mapping problem

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
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Last edited by dan; 09-18-2012 at 09:09 AM. Reason: Either end or both ends can match, and I want to return the pair.
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Old 09-20-2012, 05:00 AM   #2
TiborNagy
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Most of the aligners handle paired data in different files. I do not think it is a problem. Use BWA or other aligner program.
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Old 09-20-2012, 05:47 AM   #3
dan
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Yup, bowtie worked fine.
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fastq, illumina reads, paired end, read mapping, short read alignment

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