What to do with the generated data

[CamillePhilippeSCI]

Ask away!

Dear community,

I am quite new to this, I have performed a transcriptome analysis using epi2me labs app, My question is, what should i do after ? I have several files and I don't know where to start,
I have infected bank voles cell lines with a virus and i wanted to see the transcriptome. I have provided the reference genome and the ref_transcriptome.

Thankyou very much,

Camille

[sarahjeeeze]

Hi! It depends on what you are looking to find out - are you interested in a particular part of the transcriptome? Are you interested in the differences between your infected and non infected cell lines? Are you looking for novel transcripts? If you can be more specific I can try to provide some guidance.

[CamillePhilippeSCI]

Hi Sarah, Thankyou for your answer, Yes it would be mainly to see if there are differences between the infected and non infected cell lines, Maybe it is a bit naive but i taught that epi2me would provide the names of the genes i have in my samples when i added the ref genome and ref transcriptome ?

Camille

[sarahjeeeze]

Hi, could you provide your input cmd? Did you also provide the ref_annotation parameter that will be needed for the gene names, and did you run with de_analysis parameter and 6 samples/3 repeats? If so then you should find gene names and transcript names where avaiable in the ref_annotation in the output transcriptomes files and in the various counts files in de_analysis folder. This repository is more a place to report any bugs and let us know if there is something missing from the workflow that you need ..for general transcriptomics guidance you might want to post your questions in the community https://community.nanoporetech.com/docs/