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.

Hi,

You need to map your gene ids to KEGG pathways, but without knowing what gene id you have in your data it is hard to point you in the right direction. If you are in a model species you can retain gene names from the GTF file by adding -g or -G to you cufflinks command. Note that cufflinks is not a bioconductor software so this is not the place for discussing this, but I want to highlight that you can influence the information that you will import into R by changing options in cufflinks.

If you have gene ids from the GTF there are many tools in bioconductor that can extract necessary information. I would start by looking at AnnotationDbi or clusterProfiler that both have excellent introduction examples. If you only have access to ids generated in your cufflinks run it will require more work as you would need to use sequence similarity to known species and based on this infer KEGG annotations. To my knowledge this can not be easily done using bioconductor packages.