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Old 11-12-2015, 12:29 PM   #1
rv20
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Location: Connecticut, USA

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

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
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Old 11-12-2015, 02:56 PM   #2
blancha
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Have you made sure you were running the latest version of STAR, and adjusted the parameter --genomeSAindexNbases, as required for small genomes?
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Old 11-12-2015, 03:01 PM   #3
Brian Bushnell
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This might explain why I was not able to get STAR to run without seg-faulting when I first tried it.... hmm.
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Old 11-12-2015, 03:37 PM   #4
rv20
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yes and yes.
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Old 11-18-2015, 08:24 AM   #5
rv20
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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.
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Old 11-19-2015, 01:28 AM   #6
gringer
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I've been able to get it working for mapping to mitochondria. I did need to do some tweaking with --genomeSAindexNbases though.
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Old 11-23-2015, 10:34 AM   #7
alexdobin
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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
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bioinfomatics, microbial genome, small genome, star, star aligner

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