Hi Nancy, It is not quite clear in which steps you used the reference annotation or how these attributes were lost exactly. Cuffcompare is a tool in Galaxy - but before we go any further I think that examining the history would be the speedest path to a solution. Would you share a history with me? You can email me back the link direct to keep your data private. Please note the problematic dataset #, leaving all undeleted (or at least one complete analysis path). Here is how to share: https://wiki.galaxyproject.org/Support#Shared_and_Published_data Thanks! Jen Galaxy team On 1/21/14 5:29 PM, Yanxiang Shi wrote:

Hi Jennifer,

I did see tss_id in my results and also exon labels. The tss_id was assigned during the calculation, having the numbers tss1, tss2, etc. By saying writing codes I mean such as in the link you sent to me, there is:

"*Note: *If an arbitrary GTF/GFF3 file is used as input (instead of the/.combined.gtf/file produced by Cuffcompare), these attributes will not be present, but Cuffcompare can still be used to obtain these attributes with a command like this:

cuffcompare -s /path/to/genome_seqs.fa -CG -r annotation.gtf annotation.gtf

The resultingcuffcmp.combined.gtffile created by this command will have thetss_idandp_idattributes added to each record and this file can be used as input forcuffdiff."

but where do I can I type in "cuffcompare -s /path/to/genome_seqs.fa -CG -r annotation.gtf annotation.gtf" in galaxy? I don't know where I can find the -s... Is there a command line anywhere?

Thanks for your help!

Nancy

On Tue, Jan 21, 2014 at 9:46 AM, Jennifer Jackson <jen@bx.psu.edu <mailto:jen@bx.psu.edu>> wrote:

Hello Nancy,

The attribute sounds as if it is the correct place in the reference annotation file (the 9th field), but perhaps there are other format/content problems with the file. Do you have a tss_id? Do you have exons labeled?

This is the area of the manual that covers the formatting and usage of these attributes: http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff_input

I am not sure if I understand what you mean by input/writing codes. But if you need more help after reviewing the manual, please let us know,

Best,

Jen Galaxy team

On 1/18/14 9:06 AM, Yanxiang Shi wrote:

...

Hi all,

I've been trying to use the cufflinks-cuffmerge-cuffdiff flow to analyze my RNAseq data. However, cuffmerge lost my p_id. My p_id was originally from changing the protein_id to p_id by myself in the gtf file. The current p_id showed up in the same attributes column as gene_id in the gtf file. Does anyone know how to make it reachable by cuff? I'm using galaxy public platform. Apparently in the history people say solving the problem by writing an extra code. But I cannot find anywhere to input codes in galaxy.

Do I have to run everything on my own computer?

Thanks a lot!!!!!

Nancy

___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server atusegalaxy.org <http://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/

To search Galaxy mailing lists use the unified search at:

http://galaxyproject.org/search/mailinglists/

-- Jennifer Hillman-Jackson http://galaxyproject.org

-- Jennifer Hillman-Jackson http://galaxyproject.org