Question: Rna-Seq Analysis
0
杨继文 • 210 wrote:
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