Difference Between Edit-Distance And Mismatch In Tophat

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

tophat

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updated 13.8 years ago by Ido Tamir

• written 13.8 years ago by Wen.Huang

1 answer

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 ).

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written 13.8 years ago by Ido Tamir

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