Why can I set the minimum insert size in the PE alignment mode?
Two reasons. The first is that the current protocol tends to produce very short insert size or even overlaped two ends. The second reason is due to the algorithm used by Maq. Without setting minimum insert size helps to get slightly better, though a bit more conservative, alignment. • Merging .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
