RSEM not being executed

[adammaikai]

Version info
1.2.3
Ubuntu 16.04.6

To Reproduce
details:

• algorithm:
  aligner: star
  expression_caller: [rsem]
  analysis: RNA-seq
  description: H3-1
  files:
  • /scratch/rnaseq/H3-1_R1_001.fastq.gz
  • /scratch/rnaseq/H3-1_R2_001.fastq.gz
    genome_build: hg38
    fc_name: metadata
    upload:
    dir: ../final

Observed behavior
rsem is skipped and does not run. I still get quants from htseq-count, however. I was able to install rsem in my bcbio tools folder but actually do not see documentation anywhere about how to execute it so I am wondering if it is even possible. I executed again with expression_caller: [rsem, kallisto] and get kallisto results as well.

bcbio-nextgen-commands.log
bcbio-nextgen-debug.log
bcbio-nextgen.log

[naumenko-sa]

Hi @adammaikai !

I think there were some efforts to support rsem in bcbio 5-6 years ago:
https://github.com/bcbio/bcbio-nextgen/blob/master/bcbio/rnaseq/rsem.py

But as you mentioned it is not even getting installed:
https://github.com/chapmanb/cloudbiolinux/blob/master/contrib/flavor/ngs_pipeline_minimal/packages-conda.yaml

I think it was abandoned in favor of salmon/kallisto, see this comparison, for example:
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1526-y

SN

[adammaikai]

Thanks so much for your quick response. If at all possible I would like to submit a feature request for RSEM support. We are interested for the purpose of reproducing work from other projects.

[naumenko-sa]

Unfortunately, RSEM goes not very high on the priorities list.
Would you consider contributing code to the enhanced support of RSEM in bcbio?
We welcome PRs.

S.

[naumenko-sa]

Please feel free to re-open if somebody wants and has time to implement rsem support.