Maq error after using cutadapt

[cmawhinney]

I have some small RNA data, generated with a GAIIx, and I need to trim the adapter sequence off the 3' end. I used cutadapt, which seemed easy enough, but now I can't get the trimmed sequences to align in Maq. I keep getting this error:

maq: match.cc:569: int ma_match(int, char**): Assertion `size_l >= 12 && (size_r == 0 || size_r >= 12)' failed.

Any help would be greatly appreciated!

Thanks,

Chris.

[HESmith]

IIRC, MAQ is not designed to work with reads of different lengths. You may need to use a different aligner.