actual paired-end distances

[steuerna]

Hi,
I have got an Illumina run of paired-end 500 and 100 bases length. A couple of programs want to know minimum and maximum distance. What are reasonable values here?
There is also often the relative orientation of the readpairs, like forward forward or forward backward. Would this be forward backward for a paired-end protocol?
Thanks
steuerna

[krobison]

The actual distances will depend on your library prep.

At least some aligners will infer the distance from data; even if not, you can always align in single-end mode (perhaps on a sample of the data), compute the required statistics & then run the full-blown alignment