Question: How to form backend database (sqlite) files from Cuffdiff results (tabulat data file), so it can be used in cummeRbund
0
gravatar for oopssoni
21 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 21 months ago • written 21 months ago by oopssoni0
2
gravatar for Jennifer Hillman Jackson
21 months ago by
United States
Jennifer Hillman Jackson25k 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 21 months ago by Jennifer Hillman Jackson25k

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 16 months ago by dimitrischat0
0
gravatar for oopssoni
21 months ago by
oopssoni0
oopssoni0 wrote:

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

ADD COMMENTlink written 21 months ago by oopssoni0
0
gravatar for oopssoni
21 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 21 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 21 months ago by Jennifer Hillman Jackson25k
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