chromosome issues with hg38.gorGor6.net.axt

[James Andres Hemker]

Hello,

I am trying to use the tool axtToMaf to convert the file hg38.gorGor6.net.axt to a sing.maf file using the command below:

axtToMaf hg38.gorGor6.net.axt hg38.chrom.sizes gorGor6.chrom.sizes hg38.gorGor6.sing.maf -tPrefix=hg38. -qPrefix=gorGor6.

I am met with the following error, which I believe stems from the fact that the gorGor6.chrom.sizes file does not include a number of chromosomes/scaffolds used in the net.axt file (including the named chr10_KN196480v1_fix). 

hashMustFindVal: 'chr10_KN196480v1_fix' not found

The files hg38.chrom.sizes, gorGor6.chrom.sizes, and hg38.gorGor6.net.axt.gz were all downloaded from goldenpath today. Is there a way I could get a hold of the assembly that was used to create the hg38.gorGor6.net.axt.gz file in order to generate a new chrom.sizes? Any other solutions are also welcome.

Thank you,

James Hemker

---------------------------

James Hemker

Stanford University '21

B.S. Candidate Computer Science

[Gerardo Perez]

Hello James,

Thank you for your interest in the UCSC Genome Browser and your question about converting the hg38.gorGor6.net.axt file to a maf file.

I did reproduce your issue. We've added GRC patch/fix sequences to the hg38.2bit file (http://genome.ucsc.edu/goldenPath/newsarch.html#030519). We offer a fetchChromSizes utility which allows you to fetch chrom.sizes information from UCSC for the given assembly. The fetchChromSizes utility has been updated to grab the patched chrom.sizes file. You can find our utilities in the following directory (http://hgdownload.soe.ucsc.edu/admin/exe/), you can then find fetchChromSizes under the directory that matches your operating system. For example, here is the direct link for Linux: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes

You can run the utility on its own to see a help message, e.x.

$ fetchChromSizes
usage: fetchChromSizes <db> > <db>.chrom.sizes
   used to fetch chrom.sizes information from UCSC for the given <db>
<db> - name of UCSC database, e.g.: hg18, mm9, etc ...

This script expects to find one of the following commands:
   wget, mysql, or ftp in order to fetch information from UCSC.
Route the output to the file <db>.chrom.sizes as indicated above.

Example:   fetchChromSizes hg18 > hg18.chrom.sizes

You can create a new chrom.sizes file:

fetchChromSizes hg38 > hg38_new.chrom.sizes

Then you should be able to run the command without the error:

axtToMaf hg38.gorGor6.net.axt hg38_new.chrom.sizes gorGor6.chrom.sizes hg38.gorGor6.sing.maf -tPrefix=hg38. -qPrefix=gorGor6.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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