> 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
weeks.
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.
Best,
J.
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