Question: bed to bigBed conversion
1
gravatar for tanni93
4.2 years ago by
tanni9310
United States
tanni9310 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 • 4.6k views
ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by tanni9310

Hi Alex,

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

ADD REPLYlink modified 7 weeks ago by RamRS25k • written 4.2 years ago by tanni9310

Are you running Linux? What version?

ADD REPLYlink written 4.2 years ago by Alex Reynolds29k
2
gravatar for Alex Reynolds
4.2 years ago by
Alex Reynolds29k
Seattle, WA USA
Alex Reynolds29k 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 7 weeks ago by RamRS25k • written 4.2 years ago by Alex Reynolds29k

never mind. i made a mistake

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by melissa.ilsley20
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