STAR analysis and alignment

Question

[qudrat]

Hello everyone, Can I run STAR alignment tool on human genome using 16 GB RAM Linux system?

[Bastien Hervé]

That is a bit low for a human genome mapping according to this post (https://github.com/alexdobin/STAR)

30GB of RAM for human genome

And around 27GB of RAM for human genome on this STAR publication (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/)

STAR’s high mapping speed is traded off against RAM usage: STAR requires ∼27 GB of RAM for aligning to the human genome

But you have nothing to lose to give it a try !

Answer 1

[JJ]

try HISAT2 - they state that you can align a human genome on a desktop computer in their protocol. Note, however, that the index building will require more RAM but you can download standard indexes from their homepage.

Answer 2

[stolarek.ir]

there is option --sparse which reduces the RAM needs to 16 GB for human genome

Answer 3

[Bastien Hervé]

Actually typing : "star alignment requirements" on google give you what you need Then just Ctrl+F on publications using "require" key word

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/

STAR’s high mapping speed is traded off against RAM usage: STAR requires ∼27 GB of RAM for aligning to the human genome

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631051/

RAM requirements: at least 10 x GenomeSize bytes. For instance, human genome of ~3 GigaBases will require ~30 GigaBytes of RAM. 32GB is recommended for human genome alignments.

That will be hard with 16GB but give it a try imo !