I followed this tutorial to counts reads by exons.
After running the script, I got this error "Unexpected file format. Please use tab-delimited BED, GFF, or VCF. Perhaps you have non-integer starts or ends at line 2?"
I am not sure if the problem is the bed file because I downloaded the .bed file with many differents or all columns: Name of gene, chrom, strand, txStart, txEnd, cdsStart, cdsEnd, exonCount, exonStarts, exonEnds, proteinID, alignID
Althought I tried running with differents bed files, I got the same error.
What is the problem.