Steps to learn Next Generation Sequencing Analysis?

This is the third deep dive post to my recent post on 'How to land in an entry level Bioinformatics job/internships after graduation?'.

Recommend reading this original post first - https://lnkd.in/eDjpAEXZ

In our last post we discussed about the technical skills necessary to become a #Bioinformatician. Now we will discuss on how to learn each domain. As my area of expertise is Next Generation Sequencing, this post will be tailored for it. But you can always do the same steps in your domain of interest.

This post is focused on how to start learning the #NGS analysis? Things to keep in mind? How to improve your skills?

Note - All the tutorials mentioned here are found with a simple google search, there may be better tutorials out there.

1. Learn the Biology

I hope most of you must be having a biology degree. Just go back and refresh the genomics sections. Learn about the history of sequencing, how it evolved. Learn about #DNA, #RNA, Noncoding RNA, CpG islands, repetitive regions, central dogma, #genes, #mutations, whole genomes etc. from your text books or any online tutorials. This is a good coursera course you can check if you are new to biology - https://www.coursera.org/learn/genomics-research\

2. Learn about Technology

Illumina , Oxford Nanopore Technologies and PacBio are the major players in sequencing technology. You need to learn the chemistry behind each one (How they read ATGC from biological samples?), advantages and disadvantages of each technology, total output, best applications etc. The best way to learn all of this is through their own official websites. Look through their technotes, learn the workflow. You can also check Youtube videos if you love animations.

This is a good start to get a general overview on topics to learn - https://frontlinegenomics.com/dna-sequencing-how-to-choose-the-right-technology/'

3. Learn Glossary

Once you learn about sequencers and its applications, I would expect you to know all these terms from the below glossary! You will start hearing these terms frequently and will come handy when you start analysing the data or try to discuss analysis with your peers. https://www.illumina.com/science/technology/next-generation-sequencing/beginners/glossary.html

4. Choose your domain

Next step is to choose a domain of your choice. As I mentioned in my previous posts No one expect you to know everything! Choose a domain and master it. Have a general knowledge on other domains.

You can choose #RNASeq or #Exome or Whole genome and go deeper into it. Let's say you choose RNASeq, your first step is to read a latest publication related to RNASeq. Look how they have processed the data, outputs, figures, interpretations.

Why latest publication? You need to be updated on latest packages and tools people are using at the moment.

5. Find a free course!

Now we need to find a course which can walk you through each steps of analysis. There are a lot of free online courses available in internet or look for old workshops conducted by various universities which have a real world data for you to try out.

I found this course with a simple google search - https://scienceparkstudygroup.github.io/rna-seq-lesson/

6. Replicate Analysis

Now try to replicate the #analysis and generate the results and interpret it yourself. Try to change the parameters of various tools and see how the results are changing and try to explain it yourself.

7. Find answers from forums

If you are not able to find answer to a specific question or trying to debug an error, do a google search first with the error or question. If you are still not able to find an answer, post it in bioinformatics forums such as Biostars.org or SEQanswers .

Biostars - https://www.biostars.org/

SeqAnswers - https://www.seqanswers.com/

8. Use technical skills

You must try to use all the technical skills you have learned from last post to achieve the results. Eg. You can try to run the entire analysis in #AWS rather in your PC, try to write a shell script to reduce the steps. Think out of the box & make mistakes!

Read my last post here - https://www.dhirubhai.net/posts/athulmenon_linkedin-internships-jobs-activity-7055150574115119104-mPme

I know what I have explained in this post are not easy and cannot be finished in few days. But take your time, learn and implement slowly.

I will be posting next topic soon. If this article brought some value, comment and let me know.

Good luck!