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"
Hello,
Set the Cuffdiff tool form option "Generate SQLite" to "yes". That output can be used with CummeRbund.
Thanks, Jen, Galaxy team
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?
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/
