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
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
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