STAR errors out asking for a specific parameter

[RamRS]

Hi,

I'm running rsem-calculate-expression like so:

/path/to/rsem-calculate-expression \
        --paired-end \
        --star \
        --star-path /path/to/STAR \
        --keep-intermediate-files \
        --star-gzipped-read-file \
        {input.fq1} {input.fq2} \
        --star-output-genome-bam \
        /path/to/rsem/prepared/hg38 \
        sample_name.

But in a few samples, I run into this error:

EXITING because of fatal error: buffer size for SJ output is too small
Solution: increase input parameter --limitOutSJcollapsed

I'd really like to pass this parameter on to STAR without having to align with STAR separately. Is that possible?

Also, these samples worked fine a few months ago, and comparing the commands and versions, the only difference is that those commands used -p 8. Does that make a difference?

[pliu55]

Hi @RamRS,

It is possible to add --limitOutSJcollapse parameter. You can manually add it in rsem-calculate-expression's line 490 using:

" --limitOutSJcollapse your_new_parameter ".

where your_new_parameter represents the parameter you would like to use.

Hope it is helpful.

Best, Peng

[RamRS]

Thank you - I will add it to the source file right now. Do you think it would be possible to allow passthrough flags in a future version of RSEM?

[pliu55]

Thanks for the suggestion. I will keep this feature request in mind and hopefully add it in a future release.