Question: error in count reads by exons
0
gravatar for jleandroj
2.6 years ago by
jleandroj0
jleandroj0 wrote:

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

software error • 682 views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by jleandroj0
1

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.

ADD REPLYlink written 2.6 years ago by harold.smith.tarheel4.3k

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.

ADD REPLYlink written 2.6 years ago by jleandroj0

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.

ADD REPLYlink written 2.6 years ago by WouterDeCoster38k
1
gravatar for WouterDeCoster
2.6 years ago by
Belgium
WouterDeCoster38k wrote:

The bed file should look like this:

chr1 0   10000   ivl1
chr1 10000   20000   ivl2
chr1 20000   30000   ivl3
chr1 30000   40000   ivl4
ADD COMMENTlink written 2.6 years ago by WouterDeCoster38k
2

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

ADD REPLYlink written 2.6 years ago by genomax67k

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

ADD REPLYlink written 2.6 years ago by WouterDeCoster38k
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