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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,
João Fadista
"[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