Pipeline for GC Islands

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Britta M

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Oct 25, 2021, 2:06:24 PM10/25/21

to genome...@soe.ucsc.edu

Dear people from USCS,

I am searching for details on the calculation of the CpGIslands tracks from the VGP project.

I only found these details "this track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished)." and could you help me to understand what exactly was done?

Is there a git, with more details, e.g. (https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/doc/asmHubs) here? However for this git I would need help to find the exact script.

Thanks a lot,

Best Britta Meyer

Daniel Schmelter

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Oct 27, 2021, 5:16:30 PM10/27/21

to Britta M, genome-mirror

Hello Britta,

Thank you for contacting UCSC Genome Browser support about the CpG Island methods.

The methods section of the CpG Islands page has the complete description of the formula used to generate the data in the track. You referred to the VGP public hubs, but the methods are identical to our other CpG tracks like those in hg38:

https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cpgIslandExt

The program used is called "cpg_lh". I will share the code in an attachment until we can update the track description. It is an open-access tar file of C source code, which can be compiled and run.

cpglh$ make
...
$ cpg_lh
cpg_lh - calculate CpG Island data for cpgIslandExt tracks
usage:
cpg_lh <sequence.fa>
...

I hope this was helpful. If you have any more questions, please reply-all to genome...@soe.ucsc.edu. All messages sent to that address are publicly archived. If your question includes sensitive data, please reply-all to genom...@soe.ucsc.edu.

All the best,

Daniel Schmelter
UCSC Genome Browser

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