RNA STAR does not seem to work for microbial/small genomes

[rv20]

Hi everyone,
I am having some trouble with creating genome indexes with STAR. I double checked the manual and I am using all the correct parameters. but when I try to test the indexes of small genomes, I keep getting a segmentation fault during the run. Are there any solutions?

Thanks in advance,
-RV20

[blancha]

Have you made sure you were running the latest version of STAR, and adjusted the parameter --genomeSAindexNbases, as required for small genomes?

[Brian Bushnell]

This might explain why I was not able to get STAR to run without seg-faulting when I first tried it.... hmm.

[rv20]

yes and yes.

[rv20]

I have done both, but I can never run a read against the index STAR makes. It always seems to either run forever or have a segmentation fault.

[gringer]

I've been able to get it working for mapping to mitochondria. I did need to do some tweaking with --genomeSAindexNbases though.

[alexdobin]

Hi @rv20,

please post/e-mail the genome and the read(s) that cause the problem.
As was suggested, reducing --genomeSAindexNbases is the only thing required to run it on small genomes.

Cheers
Alex