Question: How to form backend database (sqlite) files from Cuffdiff results (tabulat data file), so it can be used in cummeRbund
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gravatar for oopssoni
9 months ago by
oopssoni0
oopssoni0 wrote:

Daer Sir, Please provide me information about "How to form backend database (sqlite) files from Cuffdiff results (tabulat data file), so it can be used in cummeRbund"

ADD COMMENTlink modified 9 months ago • written 9 months ago by oopssoni0
2
gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Set the Cuffdiff tool form option "Generate SQLite" to "yes". That output can be used with CummeRbund.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 9 months ago by Jennifer Hillman Jackson23k

could you please tell me if there is a way to put an option when you run cuffdiff from terminal so that you can get an sqlite output? or how to get the results from cuffdiff ( again by terminal ) and make an sqlite output. is there a way?

ADD REPLYlink written 4 months ago by dimitrischat0
0
gravatar for oopssoni
9 months ago by
oopssoni0
oopssoni0 wrote:

Hello, Thank you for your reply, I completed my job.

ADD COMMENTlink written 9 months ago by oopssoni0
0
gravatar for oopssoni
9 months ago by
oopssoni0
oopssoni0 wrote:

Hello, My another question about Cuffdiff result's data file. Which provide Gene ID as XLOC_id so how can change this id to ENSEMBL_id or Gene_id?

ADD COMMENTlink written 9 months ago by oopssoni0

Gene IDs come from the reference annotation incorporated into the analysis.

This prior Q&A explains more (as do many other posts - search by "Cuffdiff" + "gene" to find them) : https://biostar.usegalaxy.org/p/21827/

Example usage for reference annotation is also in the RNA-seq tutorials here: https://new.galaxyproject.org/learn/

ADD REPLYlink written 9 months ago by Jennifer Hillman Jackson23k
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