Missing CRISPR target
Ran Zhang
Dear UCSC group,
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> My name is Ran Zhang, I’m a university student who is doing research in CRISPR guide selection and design.
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> I harvested some data from the pre-computed version at UCSC website.
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> I found that there are two blank regions at two genes:NF1 and NF2 in both hg19 and hg38 assembly, but when I used your website to predict within the blank region, there are target sites exist in these region. The blank regions for hg38 are: chr17: 31105435- 31118461 and chr22: 29614087- 29626772.
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> I’m wondering if I can get the data for these two regions please.
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> Best regards
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> Ran Zhang
>
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Jairo Navarro Gonzalez
Hello,
Thank you for using the UCSC Genome Browser and your inquiry.
We do have the crispr track analysis available for the entire human/hg19/GRCh37 genome sequence. This track hasn't gone through our QA check process, so this is preliminary, so consider this temporary until we have the final verification done. You can see the areas of the genome covered in the crisprAllRanges.txt file in this directory:
https://hgdownload-test.gi.ucsc.edu/goldenPath/hg19/database/
And the crispr analysis with scores can be obtained from the crispr.bb file in this directory:
Note, these are very large files, you do not need to download them to use the data in them. The data can be extracted with the kent command line tools, available:
For example, to see the structure of the file:
To extract data from a range in the file:
The description of the track and how it appears in the genome browser can
be seen in this text:
https://genome-test.gi.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chr2&g=crisprAll
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.
Jairo Navarro
UCSC Genome Browser
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