Error in Aberrant Expression Analysis with only external counts

[bijuissac]

Hi Team

I am trying to run AE pipeline with only external counts but it gives error

Quitting from lines 62-67 [unnamed-chunk-5] (/hpcdata/scratch/25550129.1.all.q/RtmpUSQCPG/file3e615edaefc8/SampleAnnotation.spin.Rmd)
Error in file.exists():
! invalid 'file' argument
Backtrace:

1. sa[, :=(aux1, file.exists(RNA_BAM_FILE))]
2. data.table:::[.data.table(sa, , :=(aux1, file.exists(RNA_BAM_FILE)))
3. base::eval(jsub, SDenv, parent.frame())
4. base::eval(jsub, SDenv, parent.frame())
5. base::file.exists(RNA_BAM_FILE)
   Execution halted

However, if I provide even a single BAM, it seems to proceed to next step.

Does the pipeline work if we only have external counts? Does the pipeline need a BAM?

[AtaJadidAhari]

Hi @bijuissac,

Thanks for using DROP!
I checked and there is indeed a problem on how we check the non-existent RNA_BAM_FILEs. Currently if all of the samples are external, your error will occur. Thanks for noticing this, we will fix it in the next DROP release!

As a workaround, as you mentioned you can add one dummy sample and fill the RNA_BAM_FILE entry in sample_annotation file, a dummy path like test.bam will work since the BAM file doesn't need to exist. Also give that sample a different DROP_GROUP name and run the pipeline again.

[vyepez88]

Hi, to add to this, we initially designed DROP not to accept external counts only, as if you already have the count matrix of your cohort, you can simply run OUTRIDER on it in 4 lines:

1. convert the count matrix to an ods object
2. filter it
3. run OUTRIDER
4. extract the results

which is way easier than setting up DROP.