TopHat mapping qualities

[dychiang]

I've been trying out TopHat and am very impressed with the output file formats. However, I'm concerned about overly-optimistic mapping qualities. Here is a histogram of mapping qualities from the accepted_hits.sam file:

0 740658
1 900086
3 1331331
255 23028798

Some reads have high mapping qualities but can map to multiple locations:
HWUSI-EAS211R:5:43:1439:341#0 153 chr1 18448 255 35M *
0 0 GGTTTTTTTTTTTTTTTTTGCATCTATGAAGTTTT ^I`bbbabbbaaabaabbaab_Wa
aaa_ba_bbb` NM:i:3

Are there alterations to the default TopHat parameters that you would recommend to report more accurate mapping qualities, as well as more stringent alignments?


Thanks,
Derek