Question: bedTools - Genome file
gravatar for Mo Heydarian
2.6 years ago by
Mo Heydarian830
United States
Mo Heydarian830 wrote:

Hi Galaxy Community,

The bedTools tools were updated recently with some great additions. Some of these updated tools require a 'Genome file', which is a file containing the size of the chromosomes of your reference genome. This should be a two column tabular file with the chromosome name in the first column and the END coordinate of the chromosome in the second column, see an example below (for mm9):

chr1    197195432
chr2    181748087
chr3    159599783
chr4    155630120
chr5    152537259
chr6    149517037
chr7    152524553
chr8    131738871
chr9    124076172
chr10   129993255
chr11   121843856
chr12   121257530
chr13   120284312
chr14   125194864
chr15   103494974
chr16   98319150
chr17   95272651
chr18   90772031
chr19   61342430
chrX    166650296
chrY    15902555

These are the bedTools tools requiring a 'Genome file':

  • Convert from BEDPE to BAM

  • FisherBed

  • ComplementBed

  • Intersect multiple sorted BED files

  • Merge BedGraph files

  • SlopBed

  • Genome Coverage

  • ShuffleBed

  • Convert from BED to BAM

  • RandomBed

  • FlankBed

Since the reference genome is associated with files input to bedTools does it make sense to have the user input the 'Genome file' when the same information is likely available in the inner workings of Galaxy? Having the user create and recall the 'Genome file' seems like an opportunity to introduce unnecessary errors.



reference genome file bedtools • 4.2k views
ADD COMMENTlink modified 2.6 years ago by Bjoern Gruening5.1k • written 2.6 years ago by Mo Heydarian830
gravatar for Jennifer Hillman Jackson
2.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hi Mo,

This certainly seems like a way to make the usage easier. Would you like to open an enhancement request in the Bedtools Github repository for this? Or let me know and I can.

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Jennifer Hillman Jackson25k

Hi Jen, Would the bedTools Github repository be the appropriate place to open an enhancement request? Since this would be a request specific to bedTools within Galaxy, is there a Galaxy specific bedTools Github repository to post to?

ADD REPLYlink written 2.6 years ago by Mo Heydarian830

Hi Mo.

I assume Jen is talking about the IUC Github repository:


ADD REPLYlink written 2.6 years ago by Hotz, Hans-Rudolf1.8k

Thanks for the clarification, Hans.

ADD REPLYlink written 2.6 years ago by Mo Heydarian830

Yeah, it's my fault ... we can use len files from Galaxy by default and enable own files as optional step. Mo please fill a bug report at IUC.

ADD REPLYlink written 2.6 years ago by Bjoern Gruening5.1k
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