> On Thu, Mar 10, 2011 at 7:55 AM, Jeremy Goecks <jeremy.goe...@emory.edu> 
> wrote:
> Jagat,
> 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.

Hello all,

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.

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