Since the pictures are too big for the mailling list. I will upload it in seperate emails.
Dear all, I am using Galaxy for RNA-Seq analysis. I expect two lists: differentially expressed transcripts and differentially expressed genes. In these two lists, I would like to see the gene name, gene ID and transcript ID. What I did is: I run cufflinks using reference gene sets (GTF file) from Ensembl (see picture "human Chr19 refgene"). I modified the ensembl GTF file according to http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq4 so that cufflinks can recognize the column for chromosomes. I got "cufflinks assembled transcript" which shows nicely the gene ID, transcript ID (see picture "Cufflinks assembled transcript"), but the gene name was lost in this file. Then I run cuffcompare using the same reference gene sets (GTF file) from Ensembl. In the output file (picture "cuffcompare combined transcript") you can see that gene name appeared, but galaxy assigned new ID to gene and transcript. Then I run cuffdiff . Output file (see picture "Cuffdiff transcript differential expression") only contains gene name. My question is: how can I keep the information from the reference gene sets during the whole analysis process so that I get meaningful information. Or it is that possible that I retrieve "gene ID, transcripte ID" by using the output file "Cuffdiff transcript differential expression" from cuffdiff? I hope you can help me. Many thanks in advance. JIwen