How can I analyze complete human genome

Question

[lazadam]

Hello,

I m french student who's trainee in a neuroscience lab and I m stuck for months with a problem. I m explaining myself : we have eleven complete human genome, and I want to know if they are something different in those DNA like a virus who's integrated or some known mutation. For this, I did some research and I tried to blast those data in galaxy using the server of the lab. I also have two version of each genome : FastQ and FastA. Each FastQ genome weighs about 25GB and for the FastA it about 15GB so it really heavy to do something. I had an idea : just blast the entire genome of my patient with the reference human genome and look what's happen and if they are differences search what they are (viruses, mutations..) but then I had a problem : in galaxy I don't know how to get a reference human genome... I'm not at all a bioinformatician, actually I'm a medical student and I don't have the basics of tools for doing that, but I'm trying to do my best to resolve this problem and to progress in this domain with your help :)

I'm really sorry for my approximative english and I hope someone will could help me ! Thank you very much for your time !

[Pierre Lindenbaum]

I m french student who's trainee in a neuroscience lab and I m stuck for months with a problem. I m explaining myself : we have eleven complete human genome, and I want to know if they are something different in those DNA like a virus who's integrated or some known mutation.

Why do you do this all alone ?

[lazadam]

I'm not doing that alone I have the help of the members of the research team ! But it my personal project to analyze those genome in order to learn some skills in bioinformatics

[Pierre Lindenbaum]

I see. So follow genomax's suggestion: forget galaxy and learn the unix command line.

[Pierre Lindenbaum]

Some good suggestions for the lone student: https://t.co/M6wrPmXoOY , from @BioMickWatson

— Carlo SF (@CharlesColdroom) April 28, 2019

Answer 1

[GenoMax]

we have eleven complete human genome

You mention that you have fastq/fasta format data? Is that just the raw data?

There are many tutorials available for Galaxy loc 1 and loc 2. One you would be interested in would be "Calling variants ih humans" located here. If you are using public galaxy then Human genome builds (hg19 and GRCh38) should already be available. If not you can create one following directions here. GENCODE has the necessary genome reference data available.

It may be valuable to pick up some unix command line skills since that will allow you to use many other tools that may not be available in Galaxy.

[lazadam]

Yes it is the raw data ! We also have the data who are analyzed but I want to search something who isn't searched when they did the analyze (in fact I want to search some integrated virus, and I hoped that the tool "Blast" could be useful for that). Can I ask you if you know how can I do that ? Maybe I have to use the already analyzed genome to reach my goal ? I'm trying to gain some bio-informatics skills by enrolling in the bioinformatics specialization proposed by Coursera and UCSD so I hope I could do this more easily in future. Thank you for your response, your links will be valuable for my learning