Hi Jeremy,   I have been trying to use the tool mentioned in this message. I have two samples comparison  6 and 5 and has run Cufflink/ Cuffcompare/ Cuffdiff. I have filtred the files for c12 i.e for significant analysis and file is 10 uploaded as B_A Cuffdiff isoform expr filtered.txt I uploaded the second file 11 B_A_Homo_sapiens.GRCh37.60.clean.combined which is a combined GTF file generated by cuffcompare.   When I tried to run filter combined transcript file using: Combined GTF as Cufflink assembled transcripts (11)  and Cuffcompare tracking file as Cuffdiff isoform exp filtered file  using sample no as 2,  it return an empty file (12) Than thinking that perhaps it may be tracking file which I may have to use instead of combined GTF. I used B-A combined tracking file in place of combined GTF file but it will pop up only in Cuffcompare tracking file It may not be right but I used File 13 as  tracking file with combined GTF as as assembled transcript still it return empty out put I have also shared history with you.   Would you like to point me what is going on here? Thanks.     Vasu --- On Mon, 4/11/11, Jeremy Goecks <jeremy.goecks@emory.edu> wrote: From: Jeremy Goecks <jeremy.goecks@emory.edu> Subject: Re: [galaxy-user] downstream analysis of cuffdiff out put To: "shamsher jagat" <kanwarjag@gmail.com> Cc: "galaxy-user" <galaxy-user@lists.bx.psu.edu> Date: Monday, April 11, 2011, 9:04 AM On Thu, Mar 10, 2011 at 7:55 AM, Jeremy Goecks <jeremy.goecks@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. -----Inline Attachment Follows----- ___________________________________________________________ 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:   http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at:   http://lists.bx.psu.edu/