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fadista 09-02-2008 02:16 PM

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,
Joćo Fadista

zee 09-03-2008 01:07 AM


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

maq chr.bfa read1.bfq

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

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