Request of hlep- bigbed to gff output

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Huiyan Jin

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Aug 4, 2022, 11:57:49 AM8/4/22
to genome...@soe.ucsc.edu

Hello there,

 

I am in need of adding Clinvar CNV track to some genome browser for visualization and using the links included in the file for linkouts, and I am having trouble with getting to a gff file. I started with a bigbed I downloaded USCS source http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/clinvar/ 

, and managed to convert to a bed file, but still in need of gff format. Could you please point me to a gff file, or how I can convert it from a bigbed please?

 

Thank you!

 

Huiyan

 

Huiyan Jin, PhD

Senior NGS FAS

Oxford Gene Technology In

520 White Plains Road

Suite 500

Tarrytown, NY

10591, United States

 



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Gerardo Perez

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Aug 5, 2022, 9:37:40 PM8/5/22
to Huiyan Jin, genome...@soe.ucsc.edu

Hello, Huiyan.

Thank you for your interest in the Genome Browser and for your question about getting a Clinvar CNV gff file.

We do not offer the Clinvar CNV data as a gff file. But you can use the Table Browser and send the BED output to Galaxy, where you can convert bed to gff. For example, navigate to the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables):
1. Make the following selections:

clade: Mammal
genome: Human
assembly: Dec. 2013 (GRCh37/hg19)
group: Phenotype and Literature
track: ClinVar Variants
table: clinVar CNVs (clinvarCnv)

2. Set the region to “genome”
3. Set the output format to “BED - browser extensible data”
4. Select "Galaxy"
5. Click get output, then click Send query to Galaxy
6. On Galaxy, after the job finishes running, click the pencil icon
7. Under "Edit Dataset Attributes", Click Convert, then click Create Dataset
8. After the job finishes running, you can then download the dataset by clicking on the floppy disk icon

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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