I want to do differential splicing analysis using SplicingCompass (http://www.leibniz-hki.de/files/content/institut/oeffentliche_ressourcen/software/SplicingCompass/SplicingCompassTutorial.pdf).
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.