What is the gain if PE reads are in use?
More reads will get higher mapping qualities. If one read is a repeat and the other can be mapped with confidence, the repeat read can be aligned correctly and get a high mapping quality. In addition, you can use PE reads to find structural variations and short indels. • Why can’t 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
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