map files fails. What happens?
For the moment, 32-bit maq can only process files smaller than 2Gb. Possibly your alignment file is too huge for maq to handle. This is solvable. We are working on that. You can also use 64-bit version of maq. 2Gb would not be a limit. In addition, 64-bit maq is much faster than 32-bit in alignment. • Can I see the read alignment in a better viewer? Yes, you can. Please check out Maqview or tgap-maq. • Can I quickly retrieve a small region from the maq alignment? Yes, you can. Maqview provides a command-line tool, maqindex, to do this. • Are there similar alignment softwares that specifically designed for short reads? Eland, the Solexa read alignment program, can do this. It is faster than Maq actually. Maq deliberately trades the speed for several things that are not implemented in Eland. I know people also use SSAHA2, GMAP, Mosaik and SXOligoSearch to align reads. A friend of mine, Ruiqiang Li, wrote a software, SOAP, which is capable of finding short indels. On smaller data set, cro
