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-Jackson
http://galaxyproject.org
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