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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