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 resulting cuffcmp.combined.gtf file created by this command will have
the tss_id and p_id attributes added to each record and this file can be
used as input for cuffdiff."

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 <j...@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
>
>
>
> ___________________________________________________________
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> --
> Jennifer Hillman-Jacksonhttp://galaxyproject.org
>
>
___________________________________________________________
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