Difference Between Edit-Distance And Mismatch In Tophat

Question

[Wen.Huang]

Hi everybody,

I was wondering if any body knows what is the difference between the options in tophat?

-N: number of mismatches and

-read-edit-dist: number of edit distance

what would be the number of mismatches and edit distance respectively for a 2-bp indel?

Thanks, Wen

Answer 1

[Ido Tamir]

I have not played with this myself, but from what I understand from http://tophat.cbcb.umd.edu/faq.html#edit_dist

• -N/--read-mismatches:

  mismatches (i.e. only substitutions, no indels)

• --read-edit-dist:

  mismatches + indels

Then as per the FAQ entry, you can shift between wanting to exclude indels (--read-gap-length 0) and allowing indels (--read-gap-length > 0 ).