Alignment PE reads with different length by TopHat

[Trudy]

Hello!
I want to know if TopHat 1.2.0 can work with paired-end reads of different lenght without problems.
Can I modify the -r/--mate-inner-dist for correct output?

Example: I have sample with insert size of 200bp, the first read of 75bp and the second read of 50bp (for quality decrease).
Can I modify -r option as 200-(75-50)? is correct?

Are there other TopHat options that I must to consider?

Thanks in advance

Valeria

[fpepin]

Welcome Valeria,

as for your question, I'll give you the same answer I got when I asked my first question on this thread: go to the bioinformatics forum and ask there.

That's where people will read it and answer it.