FLASh parameters for 250 read length

Question

[chinjuj91]

Hi ,I would like to know what will be the best minimum and maximum overlap length parameters for FLASh if it's 250x2 paired end reads?

[gb]

No one can answer this question without knowing the length of the fragments. But FLASH gives an very informative output, so you can try different settings and check the changes. As an extra tip, a lot of times it helps to trim of a little of the bad quality ends, it can result in much more merged reads.

I use most of the time 50 bases overlap and the max I don't use (so put the max very high). FLASF gives information about that max value if it is done with merging so you can adjust it after a first try.

Answer 1

[Carambakaracho]

The answer depends on your library prep: 1000 bp fragments -> max 50 bps overlap should do the trick. 400 bp fragments -> more in the range of 200 bps max overlap, maybe even more. I never used the min overlap. Anyway I'd strongly recommend to iterate over different options.

[gb]

I only use the min-overlap and mismatch ratio. So the reads need to overlap minimal 50 bases and in that overlapping part only allow 10% errors for example.