How to start analyzing next-generation DNA and RNA sequencing data?

Question

[Ben]

Hi all,

I can find my ways around in R in windows but now want to learn to start analyzing next-generation DNA and RNA sequencing data. I'm wondering what language(s) should I learn and were should I start for the fastest learning procedure?

Thanks for the help

Answer 1

[Alice]

You can start with this book https://www.biostarhandbook.com/

If you plan to do NGS in the next couple of years, that would be a good investment.

[Ben]

Thanks. Yes, I will do NGS in the next couple of years. But do think is this the fastest way?

Thanks

[Alice]

Well, is the question "the fastest" or the "correct" way? The fastest could be to dive into the data googling your questions once they appear. It actually means that your confidence and experience will increase very slowly because you probably will have hard time understanding why these solutions work\do not work. I recommend to start with at least some introductory tutorials, you can find a lot of them on the web (most of them are free). Many tutorials have some data to play with and usually do not require a computer cluster to analyse the data. I also would recomment to sign up for a workshop or a class in computational genomics or something related (if you are ugrad or grad student).
About the language - there is also no strict recommendation. Regular pipelines require a decent familiarity with unix command line interface, R is the way to do stats and graphics, python\perl\any other language is usually helpful to know in order to write something more complicated than a regular 'grep'

[Ben]

Thanks a lot for the help.

Answer 2

[tarek.mohamed]

Hi Ben,

Do you want to exclusively use R, or you are up to other unix-based tools as well?

T

[Ben]

Hi Tarek,

Thanks for the reply. I'm only familiar with the windows but if you think unix-based tools are a faster approach, then I will start by learning unix. What is your suggestion?

Thanks

Answer 3

[geocarvalho]

As you are familiar with R, see Harvardx classes. I also recommend starting reading Biostar Handbook. Nowadays, I'm migrating my shell/python pipelines to pipeline frameworks as Nextflow and Snakemake. The Bioinformatics DotCa has an awesome channel on youtube with great classes about clinical bioinformatics.

[Ben]

Thanks a lot for the help.