error in count reads by exons

Question

[jleandroj]

Hi

I followed this tutorial to counts reads by exons.

http://bedtools.readthedocs.io/en/latest/content/tools/multicov.html

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.

Thanks

[harold.smith.tarheel]

Name of gene, chrom, strand, txStart, txEnd, cdsStart, cdsEnd, exonCount, exonStarts, exonEnds, proteinID, alignID

This appears to be refGene (or GenePred) file format, not BED. BED files must begin with the columns chromosome, start position, and stop position.

[jleandroj]

Thanks Wouter De coster and thanks genomax2

I selected in the ucsc in outformat: selected fields from primary tables and related tables and that is the reason because I was wrong when I downloaded the table.

Sorry.

[WouterDeCoster]

Please use ADD REPLY or ADD COMMENT to answer to earlier reactions, as such this thread remains logically structured and easy to follow.

We are happy that this could be solved so easily.

Answer 1

[WouterDeCoster]

The bed file should look like this:

chr1 0   10000   ivl1
chr1 10000   20000   ivl2
chr1 20000   30000   ivl3
chr1 30000   40000   ivl4

[GenoMax]

A minimal BED file should look like that. But there is BED detail format that may fit what OP has.

[WouterDeCoster]

Right, I copy-pasted the example bed from http://bedtools.readthedocs.io/en/latest/content/tools/multicov.html