Question: Data collection and Tophat2
gravatar for Philipe Moncuquet
4.0 years ago by
Philipe Moncuquet40 wrote:


I am trying to play with data collection (developped by John Chilton) and I am confused on how to do the Tophat2 step.

I have 5 conditions (triplicates) paired end data. So I have 30 files that I use to create a 'list of dataset pairs'. I end up with that new entity containing 15 pairs. It work fine for grooming, QC and trimming. But when comes the alignment step I select paired end data in tophat2 and then select the collection in both inputs. I end up with a accepted hits for each of the 30 files and not for each pair.

Now I guess I could create 2 list of datasets (1 for forward and 1 for reverse) but it seems weird as the point of collection is to handle pairs. I think I am missing something here but can't figured out what. Can someone clarifies that for me ?





rna-seq tophat2 collection • 1.0k views
ADD COMMENTlink modified 4.0 years ago by Bjoern Gruening5.1k • written 4.0 years ago by Philipe Moncuquet40
gravatar for Bjoern Gruening
4.0 years ago by
Bjoern Gruening5.1k
Bjoern Gruening5.1k wrote:

Hi Philipe,

this will be available with a new version of our TopHat wrappers:

Expect them to hit the ToolShed soon!



ADD COMMENTlink written 4.0 years ago by Bjoern Gruening5.1k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 165 users visited in the last hour