> On Thu, Mar 10, 2011 at 7:55 AM, Jeremy Goecks <jeremy.goe...@emory.edu>
> Just like any mRNA-seq experiment to achieve following objectives:
>> 1. Reconstruct all transcripts of a particular gene and corresponding
>> Cuffdiff significantly expressed transcripts as called by cuffdiff.
>> 2. What are different isoforms
>> 3. Location of splicing
>> From various output files which unique ID can be matched from one file say
>> Cuffdiff.expr (transcript/ isoform/Splicing) to other file -
>> transcript.gtf corresponding to each sample or combined GTF file.
> I've got a script that does this for the cuffdiff isoform expression testing
> file and a GTF file; I'll wrap it up and add it to Galaxy in the next couple
> weeks. It would probably be useful to have similar scripts for the other
> expression testing files as well. Also, it would be nice to be able to take
> the FPKM values generated by Cuffdiff and attach them to their respective
> transcripts as attributes.
I've added a tool called 'Filter GTF file by attribute values list' to the
galaxy-central code repository. This tool is available on our test server (
http://test.g2.bx.psu.edu/ ) at Filter and Sort --> GFF --> Filter GTF data by
attribute values list and will be available on our main server in the next few
As expected, this tool filters a GTF file based on a list of attribute
values--or filters using a tabular file where attribute values are first
column, as is the case for Cuffdiff output files. Potential attributes that can
be filtered on include transcript_id, gene_id, tss_id, and p_id; conveniently,
these are the IDs that Cuffdiff uses in its output files.
Here's an example workflow:
(1) Run Cufflinks/compare/diff
(2) Filter Cufflinks isoform differential expression file for transcripts that
are differentially expressed; in other words, filter for c12=='yes'
(2) Use 'Filter GTF data by attribute values list' to filter Cuffcompare
combined transcripts using the filtered file from step (2) as the attribute
values list and, voila, you have a GTF file of the differentially expressed
transcripts that you can view in your favorite genome browser.
Hope this helps; feedback is always welcome.
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
To manage your subscriptions to this and other Galaxy lists,
please use the interface at: