Need help with "Count intervals in one file overlapping intervals in another file" tool

Question: Need help with "Count intervals in one file overlapping intervals in another file" tool

3.9 years ago by

France

Hi,

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

Guillaume

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

Tool version: 0.1.0
Tool ID: toolshed.g2.bx.psu.edu/repos/aaronquinlan/bedtools/bedtools_coveragebed_counts/0.1.0
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/aaronquinlan/bedtools

count intervals tool bam • 3.2k views

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modified 2.6 years ago by tymiller • 60 • written 3.9 years ago by guillaume.riviere • 0

3.9 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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:
http://wiki.galaxyproject.org/Learn/Datatypes

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:
http://wiki.galaxyproject.org/Support#Error_from_tools

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

ADD COMMENT • link written 3.9 years ago by Jennifer Hillman Jackson ♦ 25k

2.6 years ago by

tymiller • 60

United States

tymiller • 60 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)?

Thanks!

ADD COMMENT • link written 2.6 years ago by tymiller • 60

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