Challenging read mapping problem

dan

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Challenging read mapping problem

09-18-2012, 09:08 AM

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

Last edited by dan; 09-18-2012, 09:09 AM. Reason: Either end or both ends can match, and I want to return the pair.

Homepage: Dan Bolser
MetaBase the database of biological databases.
Tags: fastq, illumina reads, paired end, read mapping, short read alignment
TiborNagy

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#2

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.
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dan

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09-20-2012, 05:47 AM

Yup, bowtie worked fine.

Homepage: Dan Bolser
MetaBase the database of biological databases.
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