Question: SplicingCompass: error in processing CoverageBed
gravatar for big_picture
11 months ago by
big_picture0 wrote:


I want to do differential splicing analysis using SplicingCompass (

Necessary files:

  • bam files (ideally from TopHat mapping)

  • counted read numbers using CoverageBed, aligned to all exons in union transcript (script is provided by the authors, annotation file downloaded from UCSC database; hg38, annotation file: genes and gene predictions, NCBI_Refseq, GTF; id to symbol mapping file: genes and gene predictions, NCBI_Refseq, selected fields from primary and related tables --> name and name2)

  • junction files from mapping.

I used mapping with STAR, so I converted the SJ_out files to junction.bed files using this script on github: to convert them into the right format for SplicingCompass.

I had no problems until line 38, where I got the following error message:

countTable=constructCountTable(countTable,nCores=1,printDotPerGene=TRUE) Processing CoverageBed output files: |=============== | 12% Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : scan() expected 'a real', got 'D00614:183:CABNAANXX:3:1107:7896:66038'

It is unable to process the gff files, I couldn't identify where the mistake is. Does anyone have an idea? I can provide more info about the files.

Thank you!

ADD COMMENTlink written 11 months ago by big_picture0
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