Tuxedo

[fabianomenegidio]

Hello,

Can I import transcriptome data from Tuxedo to Tbro?

I saw that they added the option of importing data from Mapman to Tbro, but I could not find information on how to do it.

Thank you.

[iimog]

Hi @fabianomenegidio

Tuxedo output is not yet supported. Can you provide an example file so I can have a look whether it can be easily implemented.

Regarding Mapman: See this section of the manual. The mapman files I used for import contain headers which are important (see this example).

If you need more help with the import of Mapman data or better documentation, let me know.

Best,
Markus

[fabianomenegidio]

Hi,

Sorry to return after so long.

I forward attached sample files from the Tuxedo package. They are divided into the output files of Cufflinks, which will exist for each replica, and Cuffdiff, which does differential data analysis.

It would be as if Cufflinks data were analogous to RSEM and Cuffdiff data analogous to DSEQ. Another interesting data would be Cuffcompare, which annotation the putative splicings.

Note: Cuffdiff data does not show results for all files because I used a simplified GFF file.

Att

Cuffcompare.tar.gz
Cufflinks.tar.gz
Cuffdiff.tar.gz

[iimog]

Hi @fabianomenegidio
good to see that you are still interested in TBro. I'm not sure at which stage you are right now? Do you have an instance set up? Do you have some data already loaded in there? Did you try to import the cufflinks/cuffdiff data? I'm happy to help but I need a little more information to know where exactly you are struggling.