Question: Hardware requirement for RNA-seq
1
gravatar for Antonio.Aubry
6 months ago by
Antonio.Aubry10 wrote:

Hi all,

I'm new to RNA-seq and am curious about what the minimal hardware requirements are for processing. I'd prefer to work with a Mac desktop if possible

Details: Organism- mouse

aligning against reference not de novo

diff expression analysis using R

hardware rna-seq alignment R • 504 views
ADD COMMENTlink modified 6 months ago by Lior Pachter370 • written 6 months ago by Antonio.Aubry10

Thanks for the answer geno, and for the links AT.

ADD REPLYlink written 6 months ago by Antonio.Aubry10

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ADD REPLYlink written 6 months ago by WouterDeCoster40k

If quantifying gene expression and performing differential expression analysis, the requirements are very small, depending on the method. See the small experiment Bioinformatics on a Rock64. However, I don't know if the same machine is sufficient to perform all steps, as the post doesn't make it clear if the human transcriptome index was built by the same Rock64, or built externally by a more powerful computer.

ADD REPLYlink modified 6 months ago • written 6 months ago by h.mon27k
4
gravatar for genomax
6 months ago by
genomax71k
United States
genomax71k wrote:

Would mainly depend on aligner you choose to use.

bwa may be the one with the lightest (~6-7 G free RAM) requirement. Other aligners will need significantly more ~30G.

Consider using salmon instead of a regular aligner (https://salmon.readthedocs.io/en/latest/index.html ) as an alternative.

That should cover the rest of the analyses.

ADD COMMENTlink modified 6 months ago • written 6 months ago by genomax71k

I would typically run TopHat2 with 8 GB of RAM and 4 cores on a cluster (and I ran STAR with similar run time a few times, even though I think it tends to use more RAM when run on a computer that has extra RAM available). However, that is with 50 bp Single-End reads: if you have paired-end reads (and want to focus more on splicing and/or mutation calling), you may need additional resources and/or time (but that also means you'll need to do a genome alignment).

I guess this really relates to Brett's answer suggesting considering use of a compute cluster, but I thought I should also say something here.

ADD REPLYlink modified 6 months ago • written 6 months ago by Charles Warden7.2k
3
gravatar for brett.vanderwerff
6 months ago by
brett.vanderwerff130 wrote:

Kallisto is really similar to salmon for "pseudo alignment", I ran it with about 8GB of RAM on human samples. I think the most demanding thing was building the RNA index, which you can get "pre-built" if you look around and probably could be run with a lot less. STAR is also really popular, but on the cusp of what is doable without moving to specialized hardware. When I played with it I could do human samples with about 32GB of RAM on a desktop after a lot of coaxing. You could move to AWS or university clusters at that point, which may be something you might be interested in anyways.

ADD COMMENTlink modified 6 months ago • written 6 months ago by brett.vanderwerff130
1

Running a transcription quantification (like Salmon or kallisto) on a local computer shouldn't be a problem.

If you had a MiSeq/MiniSeq/iSeq experiments with a lower number of total reads in a SE 50 bp polyA library (say 5-10M reads per sample), you might even be able to do a genome alignment in serial (assuming you have a 2-group comparison with triplicates) on a computer with 8 GB of RAM and 2-4 cores within one day. In that case, I do think there are benefits to being able to visualize your alignment. However, most people would probably use a cluster for genome alignments (and probably have more reads from a NextSeq/HiSeq). So, learning to submit jobs on a cluster is also a very useful skill :)

ADD REPLYlink modified 6 months ago • written 6 months ago by Charles Warden7.2k
0
gravatar for Lior Pachter
6 months ago by
Lior Pachter370
United States
Lior Pachter370 wrote:

You are right that salmon is similar to kallisto, however kallisto is faster, a relevant matter if one is working on a Mac desktop. https://liorpachter.wordpress.com/2017/08/02/how-not-to-perform-a-differential-expression-analysis-or-science/

ADD COMMENTlink written 6 months ago by Lior Pachter370
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