Pre-Made STAR Index for mm10 Mouse Genome

Question

[Nerelys]

Hello! I am currently looking for a source where I can download pre-built STAR indices for the mm10 mouse genome, as I do not have sufficient resources to generate the index myself. Is there any website available for this purpose?

[GenoMax]

as I do not have sufficient resources to generate the index myself.

If that is the case you may also run into issues with alignments. STAR will require ~30G of RAM for alignments.

Consider using salmon/kallisto in that case instead.

[colindaven]

HiSat is another RNA-seq aligner which uses less RAM.

[Nerelys]

Yes, I will consider that also. Thanks a lot!

Answer 1

[dsull]

Found this online :)

http://refgenomes.databio.org/v3/assets/splash/0f10d83b1050c08dd53189986f60970b92a315aa7a16a6f1/star_index?tag=default

You'll need to download all those individual files (chrLength.txt, SA, Genome, etc.) and put them into a directory and that directory path will be your "star index" path that you supply to STAR.

[Nerelys]

Thank you so much!