Question: Data collection and Tophat2
1
gravatar for Philipe Moncuquet
4.0 years ago by
Australia
Philipe Moncuquet40 wrote:

Hi,

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 ?

Regards,

Philip

   

 

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
1
gravatar for Bjoern Gruening
4.0 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k wrote:

Hi Philipe,

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

https://github.com/galaxyproject/tools-devteam/commit/6f9c6a330542335d6ebfaae9a77687b2ac571708

Expect them to hit the ToolShed soon!

Bjoern

 

ADD COMMENTlink written 4.0 years ago by Bjoern Gruening5.1k
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