bed to bigBed conversion
1
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
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updated 2.6 years ago by
Ram
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written 9.3 years ago by
tanni93
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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.
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Hi Alex,
My bedToBigBed is giving me this error: cannot execute binary file
Are you running Linux? What version?
FYI, this is a permissions error. You can edit the permissions and run that program with the following command:
Then you can run the program and see a usage message:
More direct documentation here: https://genome.ucsc.edu/goldenPath/help/bigBed.html
never mind. i made a mistake
If you're using MacOS, you can do an identical operation but download the Mac commands instead of the Linux: