Maq -u parameter

[dizhang]

Hi guys,

-u FILE Dump unmapped reads and reads containing more than nmis mismatches to a separate file [null]

When I set this parameter in maq for paired alignment, the dump files cannot distinguish between the two pairs and assign them the same name (Eg. Gene1/1 and Gene1/1 instead of Gene1/1 and Gene1/2). Is there a way to get proper .dump file format for paired-end alignments?

Thanks!