Issue Preparing input data sets - 3.1.2 Splice junctions file - Unsure if Sierra data or Regtools error? about sierra

[rj-patrick]

Hi Andrew,

The message indicates that regtools can't see the bam file. The regtools commands in the vignette were really just a guide - to run on the vignette bams you'll need to either copy them to your working directory or point regtools to the Sierra 'extdata' folder. You can find this on your system by typing system.file("extdata",package = "Sierra") in R.

Let me know if you have any more issues.

Cheers,

Ralph

[aerickso]

Hi! Thank you for your prompt response. I've managed to solve this and obtained output .bed files (albeit, different of a different file size than used in the Vignette).

Regardless, I can now run my own files!

I needed to mount a volume which the regtools docker could access, copied the Vignette .bam and .bai files there, and then was able to successfully run regtools.