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VCCRI / Ularcirc

An R-shiny app that provides backsplice and canonical splicing analysis for both circular RNA (circRNA) and parental transcripts
GNU General Public License v3.0
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Chimeric File Crashes Ularcirc #7

Closed DarioS closed 4 years ago

DarioS commented 4 years ago

To enable STAR's chimeric output files to work with STAR-Fusion, the option --chimOutJunctionFormat 1 is used. Loading such a file into Ularcirc causes the application to crash with a traceback

Detected 21 column names but the data has 20 columns. Filling rows automatically. Set fill=TRUE explicitly to avoid this warning.
Warning: Error in : non-numeric argument to binary operator
  78: FilterChimeric [/dskh/nobackup/biostat/Bioconductor/Ularcirc/shiny-app/circRNA/Server.R#979]
  74: LoadJunctionData [/dskh/nobackup/biostat/Bioconductor/Ularcirc/shiny-app/circRNA/Server.R#733]
  73: observeEventHandler [/dskh/nobackup/biostat/Bioconductor/Ularcirc/shiny-app/circRNA/Server.R#1847]

I don't know if that's related to the crash, but it's the only difference to the default output I can think of.

davhum commented 4 years ago

Hi Dario,

Thanks for bringing this to my attention. The new chimOutJunctionFormat introduces more columns and this caused the error. Have fixed error in latest update. Still need to re-work documentation so will leave this thread active until then.

DarioS commented 4 years ago

Ah, yes, the latest version stalls when it hits a browser() so still some code to modify before release.

davhum commented 4 years ago

Documentation has been updated along with a new section in vignette.