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Old 09-02-2008, 01:12 PM   #1
fadista
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Location: Malmö

Join Date: Sep 2008
Posts: 37
Default Maq and indel discovery

I am using solexa paired-end data and after I mapped my reads with the MAQ software to a reference sample 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

Last edited by fadista; 09-02-2008 at 01:13 PM. Reason: forgot to put the software that I used
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