Question: Need help with "Count intervals in one file overlapping intervals in another file" tool
gravatar for guillaume.riviere
3.1 years ago by
guillaume.riviere0 wrote:


I'm using Galaxy public on a windows computer. The 'Count intervals in one file overlapping intervals in another file' tool displays error messages on file format in the history log, although I submit galaxy-generated or converted files that seem to me.

'Unexpected file format. Please use tab-delimited BED, GFF, or VCF. Perhaps you have non-integer starts or ends at line 1?

Any hint ?

Thanks al ot


Tool name: Count intervals in one file overlapping intervals in another file

Tool version: 0.1.0
Tool ID:
ToolShed URL:

count intervals tool bam • 2.9k views
ADD COMMENTlink modified 22 months ago by tymiller60 • written 3.1 years ago by guillaume.riviere0
gravatar for Jennifer Hillman Jackson
3.1 years ago by
United States
Jennifer Hillman Jackson24k wrote:


Double check format and remove anything out of specification: empty lines, partial lines, header lines (# lines or just column labels), mismatches in chromosome names between the inputs, etc. Use the tools in the group "Text Manipulation" to help. These can cause problems, as can other issues, but it is hard to tell which one with the information given. Even if you posted a small snippet of the datasets, it wouldn't necessarily help.

Try comparing to the format specifications here:

Then click on the pencil icon for the dataset and confirm that the columns assigned are the ones you want to use. You can also "Cut" out just the columns needed.

More troubleshooting help is here:

Hopefully this helps - but let us know if you still have problems, Jen, Galaxy team


ADD COMMENTlink written 3.1 years ago by Jennifer Hillman Jackson24k
gravatar for tymiller
22 months ago by
United States
tymiller60 wrote:

Hi, I also had a question with this tool. A clarification really. This counts overlaps (in my case from a BAM file overlapping a bed file loci). How is the overlap counted? Is it any read in the BAM file (input A) that overlaps the loci (input B) by at least 1 bp?

The other question: is every loci in the bed file considered separately? As in if I have two transcripts for the same gene the overlap each other exactly, will they both get the same amount of reads counted as overlap? And is this the same as if there had only been one transcript in the location ( e.g. does it divide the reads amongst the two transcripts if there are two and give each half)?


ADD COMMENTlink written 22 months ago by tymiller60
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