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.
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Alignment PE reads with different length by TopHat
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
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