No MAF option available for Zoonomia Cactus alignment

[Kathleen Keough]

Hello,

I'm trying to extract part of the Zoonomia Cactus 241-way alignment for a particular gene from the Table Browser, but unlike for the UCSC alignments where MAF is an option for output format, MAF is not an output format option for the Cactus alignment. Is this intentional?

Thank you,
Kathleen

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Kathleen Keough, PhD

Senior Scientist | Computational Biology

Fauna Bio | faunabio.com

[Gerardo Perez]

Hello, Kathleen.

Thank you for your interest in the Genome Browser and for bringing our attention to this bug.

The MAF output format should be an option. We have fixed the bug, however, the fix will not reach our live site until our next version release on Dec 14th. In the meantime, you can use the Table Browser with the fix in place on our development site: http://genome-preview.soe.ucsc.edu/cgi-bin/hgTables

Please note the data and tools on our development server are under development, have not been reviewed for quality, and are subject to change at any time.

I hope this is helpful. Let us know if you experience any other bugs or issues.
For 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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[Gerardo Perez]

Hello, Kathleen.

Thank you for using the UCSC Genome Browser and reporting your issues.

You have discovered a bug on our development site. We were able to reproduce the error using the region option on the Table Browser. We have fixed the bug, however, an engineer of ours shares that getting a MAF output format from the Table Browser for this huge track could lead to website timeouts.

A better option would be to use the bigBedToBed utility with a bit of code. You can download the bigBedToBed utility from the downloads page, https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads. You can then find bigBedToBed 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/bigBedToBed

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

$ ./bigBedToBed
bigBedToBed v1 - Convert from bigBed to ascii bed format.
usage:
   bigBedToBed input.bb output.bed
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
   -maxItems=N - if set, restrict output to first N items
   -udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs
   -header - output a autoSql-style header (starts with '#').

You can then run bigBedToBed with the following code but you would need to specify -chrom=___ -start=___ -end=___ for the region of interest and update the output.maf file name:

$ ./bigBedToBed http://hgdownload.soe.ucsc.edu/goldenPath/hg38/cactus241way/cactus241way.bigMaf \
stdout -chrom=chrX -start=15560138 -end=15602945 | cut -f 4 | tr ';' \
'\n' > yourOutput.maf

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

On Wed, Nov 17, 2021 at 6:32 PM Kathleen Keough <kath...@faunabio.com> wrote:

Hi Gerardo,

After working with these files a bit, I realized the whole file does not download properly, and terminates with this:

---------------------------------------------------------------------------
Too many open files
mustOpenFd: Can't open ../trash/udcCache/https/hgdownload.soe.ucsc.edu/goldenPath/hg38/cactus241way/cactus241way.bigMaf/sparseData to append
---------------------------------------------------------------------------

On Wed, Nov 17, 2021 at 2:38 PM Kathleen Keough <kath...@faunabio.com> wrote:

Hi Gerardo, 

This is a huge help, thanks!

Kathleen