Equipment for bioinformatics.

Question

[tsomakiank]

Hello to everyone! I am considering starting a masters in bioinformatics next year. I also have to analyse some RNA-seq data for my current thesis study. I have minor knowledge in computer science, so I am wondering if my laptop can handle such analysis. I have an HP EliteBook Folio 1040 in which I will install ubuntu. (ram-> 8gb/ssd->256gb/cpu->i5). Is these specs enough to begin with the RNA-seqs and upgrade later? Should I upgrade at all? If yes any idea on what?

[GenoMax]

It will depend on the size of the genome you are working with. e.g. with human transcriptome, your laptop spec is just enough to use a mapping method like salmon without using the genome decoy sequence (where salmon will need more on the order of 15-20G RAM). You may be able to use subread or bwa, if you want to use an alignment based methods. Most other aligners will not work for human genome since they need anywhere from 30-40G of RAM.

Answer 1

[nhaus]

For the master itself, I would say that it is enough (my laptop has similar specs). Maybe upgrade the RAM if you can to 16GB. For your education, you will rarely have to analyze large datasets. Usually they are broken down to small portions which can be quickly executed on a modern laptop.

As for the rna seq data that you are analyzing right now, it really depends on how big it is and if it is single cell or bulk sequencing. If you are doing your thesis at a research institute, you will also often have access to a high performance computing cluster or a workstation. To run your analysis there, you do not need a fancy laptop.

[tsomakiank]

Thanks a lot for your help nhaus