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  • 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

  • #2
    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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    • #3
      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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      • #4
        yes and yes.

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        • #5
          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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          • #6
            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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            • #7
              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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