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Old 01-04-2013, 07:58 AM   #1
Pradhaun
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Location: US

Join Date: Nov 2011
Posts: 16
Default Tophat: options -N --read-edit-dist --read-gap-length

Hi all,

I am using tophat for an alignment. I would like to know how -N option and the other two options --read-gap-length and --read-edit-dist are related.

I gave -N 6 --read-edit-dist 6 when I was aligning the sequence. I am not sure whether I have to mention --read-gap-length also or not?

Please provide your suggestions.

Thank you
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