New to bioinformatics : processing FASTQ files.
Hi I'm really new to bioinformatics, I know it is really a beginner question but how where do I process a file in this case FASTQ, is it in python or through the command line? I've been told to follow the steps in GATK website but I do not know which patform to use.
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You're asking the wrong question.
Python is just a programming language, you could use it or any number of others - in fact, you probably will use several day-to-day once you get used to it. You will almost certainly need to get comfortable on the command line.
What do you actually want to do with your FASTQs? Presumably you're trying to assemble a genome or something? But we need more information. There are a lot of different things that could all be valid answers to your queries.
Thank you for your answer, I was given a vcf file which relates to a germeline in an expanded exome from which the SNPs were processed, my task is to now processes Indels. From what I got from your answer is that I work on the command line (in my case linux terminal) and when I need it I call python? Am I close?
Python is one of the
hows. You need to focus on thewhat- What do you need to do on a granular level, that is. Once you are clear on that, look for tools (of which python is one) that can perform these tasks for you.I want to process Indels from several populations, see their variability and their validity. These indels come from a expanded human exome.
Everyone who works with variants wants to "see their variability and their validity". That is a very broad question. There are thousands of studies that attempt to do that.
Find a study that does something that you would like to replicate. Check their methods. There will be many steps.
For each step, try to perform it. If you can't, try to search for the instructions. There is a good chance that there is a previous post here with the same problem.
In the comments, you say:
In the original question, you said:
FASTQ and VCF are very different files. You should clarify your question. Do you want to process a FASTQ or a VCF? If you don't know the difference, that should be the question.
I'm going to point you to the Biostar Handbook. This should help you learn the basics of bioinformatics.
You're looking at "FASTQ" and "VCF" files. First off, you need to understand what
readsare, and howFASTQfiles record them, and then whatvariantsare, and howVCFfiles record them. Once you grasp that, you will need to understand howFASTQrecords (reads) can be eitheralignedorassembledto get closer to obtaining aVCFfile ofvariants. This is whereGATKcomes in (along withsamtools,bwa, etc)Unless you understand the underlying concepts, dabbling with these files will only serve to confuse you further.
Hello hdtms !
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It is unclear what you are asking, if you are a beginner, try to find out what you want to do exactly first.
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