Question: bed to bigBed conversion
2
gravatar for tanni93
5.2 years ago by
tanni9320
United States
tanni9320 wrote:

Hi all,  

I am having trouble converting a bed file into a bigBed file --> how many I do this without much programming?

Thank you,

Tanni 

 

 

 

 

 

rna-seq • 6.1k views
ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by tanni9320

Hi Alex,

My bedToBigBed is giving me this error: cannot execute binary file

ADD REPLYlink modified 13 months ago by _r_am32k • written 5.2 years ago by tanni9320

Are you running Linux? What version?

ADD REPLYlink written 5.2 years ago by Alex Reynolds31k

FYI, this is a permissions error. You can edit the permissions and run that program with the following command:

chmod +x ./bedToBigBed

Then you can run the program and see a usage message:

./bedToBigBed
bedToBigBed v. 2.8 - Convert bed file to bigBed. (bbi version: 4)
usage:
   bedToBigBed in.bed chrom.sizes out.bb
...

More direct documentation here: https://genome.ucsc.edu/goldenPath/help/bigBed.html

ADD REPLYlink written 5 weeks ago by danielschmelter90
3
gravatar for Alex Reynolds
5.2 years ago by
Alex Reynolds31k
Seattle, WA USA
Alex Reynolds31k wrote:

If you're using Linux, you can grab a couple of the UCSC Kent tools:

$ wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed
$ wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes

Make them executable:

$ chmod +x ./bedToBigBed ./fetchChromSizes

Fetch a chromosome size file for your build of interest (e.g., hg19 or hg38):

$ ./fetchChromSizes hg38 > hg38.chrom.sizes

Sort your BED file, for instance, with BEDOPS sort-bed:

$ sort-bed regions.unsorted.bed > regions.bed

Convert to bigBed:

$ ./bedToBigBed regions.bed hg38.chrom.sizes regions.bb

You might specify additional options for conversion; run bedToBigBed on its own for more information.

ADD COMMENTlink modified 13 months ago by _r_am32k • written 5.2 years ago by Alex Reynolds31k

never mind. i made a mistake

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by melissa.ilsley20

If you're using MacOS, you can do an identical operation but download the Mac commands instead of the Linux:

$ wget http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedToBigBed
$ wget http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/fetchChromSizes
ADD REPLYlink written 5 weeks ago by danielschmelter90
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