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
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!
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:
> 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,
> 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!!!!!
> The Galaxy User list should be used for the discussion of
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> Jennifer Hillman-Jacksonhttp://galaxyproject.org
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:
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
To search Galaxy mailing lists use the unified search at: