--limitGenomeGenerateRAM not an available option for rsem-prepare-reference

[afreed...@gmail.com]

running v 1.3.1, when trying to build an index with star, I get a rather standard STAR error in the log file:

EXITING because of FATAL PARAMETER ERROR: limitGenomeGenerateRAM=31000000000is too small for your genome

Unfortunately, at least from the rsem-prepare-reference help, there doesn't seem to be any way to add this to the rsem-prepare-reference pipeline.

is this correct and if so, besides "why?", what would be the recommended work-around? i was under the impression that I couldn't just feed in transcriptome coordinate bam files generated with star using an index build outside of rsem, i.e. I had to use rsem to build the star index. correct or not?

thanks,

adam

[Peng]

Hi Adam,

Thanks for bringing up this question.  You can build STAR index outside of RSEM and run STAR to do the alignment.  After that, you can feed STAR's BAM alignment file to RSEM for quantification.  Alternatively, if you are comfortable with Perl, you can add STAR's limitGenomeGenerateRAM option in rsem-prepare-reference anywhere between line 187 and 194 (https://github.com/deweylab/RSEM/blob/e4dda70e90fb5eb9b831306f1c381f8bbf71ef0e/rsem-prepare-reference#L187).

Best,

Peng