Nanopore tutorial for beginners

Question

[Lila M]

Hi there,

I am interested in learn how to analyzed nanopore data. I have experience in RNA-seq, ChiP-seq, microarray.... but not in ONT. I would like to ask for tutorials, papers or pipeline that have helped you to understand how to process this data and how to deal with downtream analysis. I've found a lot of information but, honestly I don't know which are the most common, the better and most efficient tools.

Any suggestion and literature would be appreciated

Thanks

[colindaven]

Sketch out what you want to achieve, this is too vague and tools are different for each application.

[Lila M]

Actually I don't have any data, I want to read and try to understand and know the tools and different tutorial/pipelines available in order to learn a bit more. This is why I asked for tutorial and literature, not for pipeline, for that reason my is not too vague

Answer 1

[GenoMax]

Data analysis is going to be slightly different for different applications but in general nanopack (LINK) should have everything you need to do QC on your samples.

If you are not a member of nanopore community then become one. Other wise the data is in fastq format (assuming you are working with basecalled data) and can be treated just like any other high-throughput sequencing data. There are threads on biostars that recommend specific packages based on application so be sure to search when you have a specific need or ask a new question.