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big_picture 04-21-2017 01:52 AM

SplicingCompass: error in processing CoverageBed files
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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:

Number of input files ok?
[1] TRUE
> countTable=new("CountTable")
> countTable=setExperimentInfo(countTable,expInf)
> 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 I made a mistake. Could you help me with it, please?

See the examples attached.

Thank you for the help!

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