MAQ and indel detection

fadista · 09-02-2008, 02:16 PM

I am using solexa paired-end data and after I mapped my reads to a reference sample with the MAQ software a message appears on the screen:
"[maq_indel_pe] the indel detector only works with short-insert mate-pair reads".
I am working with fragment sizes that have an average length of 315 bp and in the parameters -a and -A of the 'match' function I put the number 350.

My question is what does this message mean and am I not able to detect indels and, if not, why is that?

Best regards,
João Fadista

zee · 09-03-2008, 01:07 AM

Hi.

I've seen that message with single-end read alignments i.e.

maq out.map chr.bfa read1.bfq

So perhaps it's assuming that you didnt submit the other read2.bfq mate-pair file.

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09-02-2008, 02:16 PM	#1
fadista Member Location: Malmö Join Date: Sep 2008 Posts: 37	MAQ and indel detection I am using solexa paired-end data and after I mapped my reads to a reference sample with the MAQ software a message appears on the screen: "[maq_indel_pe] the indel detector only works with short-insert mate-pair reads". I am working with fragment sizes that have an average length of 315 bp and in the parameters -a and -A of the 'match' function I put the number 350. My question is what does this message mean and am I not able to detect indels and, if not, why is that? Best regards, João Fadista

09-03-2008, 01:07 AM	#2
zee NGS specialist Location: Malaysia Join Date: Apr 2008 Posts: 249	Hi. I've seen that message with single-end read alignments i.e. maq out.map chr.bfa read1.bfq So perhaps it's assuming that you didnt submit the other read2.bfq mate-pair file.