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Old 11-16-2017, 02:16 AM   #1
PierBJX
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Location: Cranfield

Join Date: Nov 2017
Posts: 1
Question KEGG with pathview using CuffDiff data

Hey everybody,

I am a newbie in coding in Bioinformatic and I have a question.

Using a HPC I perform a quality control and a read alignment with CuffLinks. At the end, I have a folder with CuffDiff. I open it with R using readCufflinks (library cummeRbund). And now I am trying to perform the metabolic pathways related to development (starch and sugar metabolism, Ethylene for example) but I don't know how to do it. I try with "pathview" but it doesn't work.

Indeed, I have to find the kegg number or accession number but I don't know how to find it from the data of CuffDiff. Do you have any hints?
Only hints that I find is on MicroArrays and it's not like me...

Thanks for your help,
Best regards.
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cuffdiff, cufflink, kegg, r programming, rna-seq

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