Filter for canonical chr

[Sampath, Srirangan]

HI,

    I am trying to pull RefSeq data into Galaxy Browser from UCSC Table Browser. I want only canonical chromosomes, and do not want alt or fix patches. I tried the filter function, and it doesn’t seem to work.

 

I tried “chr chr2..” space-separated in the ‘chrom’ window. I also tried chr? chr?? in chrom window.

 

I also tried SQL query. You have an example for chrom NOT LIKE "chr??" - restricts search to chromosomes 1 - 9, X and Y

Do you have something similar for canonical chromosomes only?

 

 

Additionally, is there a way to query in Table Browser for

1. OMIM disease related RNA genes only (described in OMIM)
2. miRNA gene with clinical evidence/or in ClinVar

 

Thanks for the help.

 

Sri.

 

Srirangan Sampath, PhD, FACMG

Director of Development, Molecular Diagnostic Laboratory

Department of Pathology and Laboratory Medicine, Children’s National Hospital

Work: 202-545-2721 (Phone)

ssam...@childrensnational.org

 

 

Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

[Sampath, Srirangan]

Hi,

    I have one more request.

 

Is there also a way I can pull down hg38 genome coordinates for 100bp around ClinVar P/LP variants?

 

Thanks
Sri.