Question: Looking for prebuilt STAR index for hg19. STAR Genome site is down.
0
gravatar for syrez
6 days ago by
syrez40
Chicago
syrez40 wrote:

Can someone please help me find a prebuilt STAR index? The page hosting pre-made indexes available at STAR Genomes site has been 404 for last few days.

rna-seq star chip-seq • 74 views
ADD COMMENTlink written 6 days ago by syrez40

You can easily generate these indexes on your own. See STAR manual for more info.

ADD REPLYlink written 6 days ago by genomax80k

Normally I would but I don't have access to an HPCC right now. I'm stranded with my laptop which has only 16gb. STAR should have worked with "--genomeSAsparseD 3 --genomeSAindexNbases 12" but the run gets killed few minutes into ".. sorting Suffix Array chunks and saving them to disk..."

ADD REPLYlink written 6 days ago by syrez40
1

If you are unable build the index on your laptop you will likely not be able to align with pre-built indexes either.

ADD REPLYlink written 6 days ago by genomax80k

Thanks, I don't need it for alignment. I simply wanted to know if there are any other shared resources where I can find the index.

ADD REPLYlink written 6 days ago by syrez40

I see. If you create an issue at STAR GitHub site Alex Dobin should get notified. I don't think there are other public download sites that I know of.

ADD REPLYlink written 6 days ago by genomax80k

You can use nf-core/rnaseq pipeline. The indices will be downloaded from their s3 iGonomes copy.

ADD REPLYlink written 6 days ago by Asaf7.2k
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