Question: Having issues using UCSC kent tools to convert bigwig file to wig file
0
gravatar for Uday Rangaswamy
11 months ago by
Indian Institute of Technology, Madras, India
Uday Rangaswamy120 wrote:

I'm trying to convert a bigwig file to wig file using UCSC kent tools and I'm following the instructions mentioned here. On entering mkdir ~/bin/$MACHTYPE on the command line I get the following error :

mkdir: cannot create directory ‘/home/uday/bin/x86_64-pc-linux-gnu’: No such file or directory.

How do I go about this? Thanks.

sequence software error • 368 views
ADD COMMENTlink modified 11 months ago by genomax76k • written 11 months ago by Uday Rangaswamy120
1

Maybe try this:

mkdir ~/bin/
mkdir ~/bin/$MACHTYPE
ADD REPLYlink written 11 months ago by Kevin Blighe53k

It solved that particular issue but faced other problems in the later steps. Thanks for your time :).

ADD REPLYlink modified 11 months ago • written 11 months ago by Uday Rangaswamy120
2
gravatar for genomax
11 months ago by
genomax76k
United States
genomax76k wrote:

Save yourself the trouble and get the compiled versions for your OS. Linux or macOS.

ADD COMMENTlink modified 11 months ago • written 11 months ago by genomax76k
1

Seconding this answer. Also here is the top directory with previous versions of the utilities: http://hgdownload.soe.ucsc.edu/admin/exe/

Here is the example location of the bigWigToWig location for linux: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigWigToWig

Running any kent util on the command line with no statement prompts the help message:

$ bigWigToWig 
bigWigToWig - Convert bigWig to wig.  This will keep more of the same structure of the
original wig than bigWigToBedGraph does, but still will break up large stepped sections
into smaller ones.
usage:
   bigWigToWig in.bigWig out.wig
options:
   -chrom=chr1 - if set restrict output to given chromosome
   -start=N - if set, restrict output to only that over start
   -end=N - if set, restict output to only that under end
   -udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs
ADD REPLYlink written 11 months ago by Luis Nassar290

Trying to convert the resulting .wig file to .bed file using :

convert2bed --input=wig [--output=bed] < hg38.phyloP4way.wig > hg38.phyloP4way.bed

Not working though. I get a memory warning while the command runs. Any thoughts? Please help.

ADD REPLYlink modified 10 months ago • written 10 months ago by Uday Rangaswamy120
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