Question: How To Create A Bigwig File And Display It
0
gravatar for rig
5.6 years ago by
rig20
Israel
rig20 wrote:

Hi all, I have a matlab file (lets assume its a struct) which contains information on the human dna, meaning that for each chromosome I have an array of data. I want to convert this matlab file to a bigWig (why this specific file format? To my understanding it saves up storage) file format, and ultimately display it as a custom track on UCSC genome browser. So:

  1. How can I convert my matlab (struct) file to a bigWig file?
  2. How can I display it as a custom track on UCSC genome browser?

Thanks!

bigwig • 4.5k views
ADD COMMENTlink modified 5.6 years ago by Devon Ryan91k • written 5.6 years ago by rig20
2
gravatar for Devon Ryan
5.6 years ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

I've never actually seen documentation on the bigWig format, people often just create a wiggle file and then use wigToBigWig. The wiggle format itself is quite simple, since it's text based, so simply iterating over your array should suffice. I'm not very familiar with matlab anymore, but you might be able to create a named pipe as the output and simply use that to directly feed input into wigToBigWig (at least that's how one would do this in C or another language). That would save disk space and probably be a bit faster if you have a few CPU cores to use.

For displaying the results on the UCSC genome browser, see this page on the FAQ.

ADD COMMENTlink written 5.6 years ago by Devon Ryan91k

Thanks, got it!

ADD REPLYlink written 5.6 years ago by rig20
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