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  • SplicingCompass: error in processing CoverageBed files

    Hey,

    I want to do differential splicing analysis using SplicingCompass (http://www.leibniz-hki.de/files/cont...ssTutorial.pdf).

    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:
    Short bash script to convert STAR SJ.out.tab into BED format similar to TopHat junctions.bed - SJtoBED12.bash

    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!
    Attached Files

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