parameters for different reads length

[liuxq]

for bowtie, default parameter for seedlen is 28, maqerr (max sum of mismatch quals across alignment) is 70.

what is the default reads length for there parameters? How to change the default parameters setting for different reads length?

[simonandrews]

We've certainly found that default bowtie parameters don't work well for longer reads in some cases. This is especially true if the quality of your sequence falls away towards the end of each read.

Generally the parameters for the seed region are OK and are still sensible for longer reads, but the sum of mismatches can cause problems. The difficulty is that there is no concept in the parameters of quality decreasing with length, so if your qualities fall too far you have to increase the mismatch sum to such a large value that it's no longer useful.

I'd advise looking at the quality plots for your sequences to see if it's worth using all of the sequence you have. If the quality is universally poor from some point then you might want to trim all of your sequences at that point. You could also consider trimming each sequence individually if there's a lot of variation in the point at which the qualities drop.

Once you have a dataset with generally good quality you'll hopefully find that the default bowtie parameters aren't so bad. You may want to increase the mismatch sum a bit, but you shouldn't need to raise it to a very high level.

One final point - make sure you're specifying the correct quality encoding scheme in the bowtie parameters since this can affect your mismatch sum results if it's set incorrectly.

[liuxq]

thanks very much