discordant paired-end reads

[sathish]

Hi Everyone,

May be a simple question, but I am having trouble finding it. I did extensive search for weeks and finally, seeking your help.

I have solexa paired-end sequences. I am trying to find the discordant paired-end reads. I used MAQ and output the unmapped reads. Are they the discordant pairs or should I find the discordant pairs in mapped reads of MAQ?

Is it possible to use BOWTIE or BWA to find discordant pairs? If so, what option should I use?

Any help will be appreciated.

Thanks,

Sathish

[john_mu]

This is just a suggestion of the top of my head so it might not be correct.

Maybe you could manually reverse-complement one side of the pairs with a small script and then align these modified pairs with a standard aligner?

[GoneSouth]

With 'bwa aln' and 'bwa sampe' its very easy to find those pairs. Using a bit of perl even different categories of discordant pairs may be easily identified like:
mates on different chromosome
mates on the same strand
mates with a weird distance
etc