Cuffdiff output ID list for gene ontology analysis in Panther

Question

[CandiceChuDVM]

Hi all,

I have finished my test run of RNA-Seq analysis with Tuxedo suite tools.

According to Panther: "The first column must be the gene or protein identifiers. See below for the supported IDs. A second column of numerical values is required if a user wants to run the statistical enrichment test."

(1) Are there suggested commands for making Cuffdiff's output into the ID list for Panther?

(2) Also, I assume the first column should be gene column but I am not sure about the what should be the numerical values in the second column? Should I use htseq to get the number of reads pre gene?

Answer 1

[CandiceChuDVM]

Hi all,

I finally figure it out! I can use R package "biomaRt" to solve my problem.

In order to benefit other users, I put the R script "biomart_refseq2ensembl.R" here:
https://github.com/candicechu/RNAseq_newbies/blob/master/biomart_refseq2ensembl.R

I hope it's not a way too stupid solution. Please let me know if you have any suggestions.

Thanks!