Finding BAC clones in your browser

[Liu, Chengyu (NIH/NHLBI) [E]]

I am interested in finding BAC clones that span a particular genomic locus.  I remember I could simply change a BAC icon from Hide to Full near the bottom of the page, and then all BAC clones will appear in the main window.  Now, I could not find the BAC icon.  Do you know how can I find BAC clones from your browser?

 

Thanks,

 

Chengyu Liu, Ph.D.

National Heart, Lung, and Blood Institute

National Institutes of Health

Tel: 301-435-5-34

[Jonathan Casper]

Hello Chengyu,

Thank you for your interest in the BAC clones track. We still have a track with BAC end pair data for the GRCh37/hg19 release of the human genome assembly, but we have not yet released a version of that track for the new GRCh38 assembly. We do, however, plan to release that track in the near future. For now, one of our engineers suggests that a work-around is to view the desired BAC in hg19, and use the view in hg38 function to see if it is still there. You can do this by selecting "In Other Genomes (Convert)" option from the "View" menu of the UCSC Genome Browser. Another option is to use the 'Hg38 Diff' track from hg19 to see if the same region is in hg38 or not. Please note that the 'Mapping' set of track controls is collapsed by default on hg19. You will need to expand that set of tracks to be able to turn on the 'Hg38 Diff' track.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

--
Jonathan Casper
UCSC Genome Bioinformatics Group

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[Pieter J. de Jong]

Chengyu,

 

One additional suggestion with respect to finding (human) BAC clones in hg19.  As you may know, the RP11 BAC library was created in my lab and can be show on the UCSC hg19 assembly Browser as indicated by Jonathan Casper.   We have another human BAC library, which can be uploaded as a custom track (the CHORI-17 “haploid” human BAC library), with insert sizes averaging ~200 kb. The haploid human assembly from the same source DNA is accessible (or will soon be) as a platinum human genome assembly (work at WashU and others).  You can upload the CH17 BAC track into the hg19 assembly using the following instructions, from our CHORI-17 library page (https://bacpac.chori.org/library.php?id=231)

 

How can one find the CHORI-17 BAC clones displayed within the UCSC Browser? Please, first upload (by Copy & Paste) the following links to the UCSC Browser Custom Track Upload: "http://bacpac.chori.org/download/ch17_hg18/ch17.bed" for the hg18 human genome assembly or "http://bacpac.chori.org/download/ch17_hg19/ch17.bed" for the hg19 human genome assembly. After uploading, the CHORI-17 BACs will only be visible for a limited time. So, you may have to repeat this.

 

Pieter J. de Jong

BACPAC Resources Center (BPRC)

Children’s Hospital Oakland Research Institute (CHORI)

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[Liu, Chengyu (NIH/NHLBI) [E]]

Thank you very much for the information. At this time, I am mainly interested in finding mouse BACs for making transgenic mice. I have already found a few suitable BACs using the older version of genome as suggested by Jonathan. Dr. Xiaoli Chen will probably order these BACs from BACPAC Resources soon. Best regards, Chengyu

From: "Pieter J. de Jong" <pde...@chori.org<mailto:pde...@chori.org>>
Organization: CHORI
Reply-To: "pde...@chori.org<mailto:pde...@chori.org>" <pde...@chori.org<mailto:pde...@chori.org>>
Date: Wednesday, August 6, 2014 at 6:55 PM
To: "Liu, Chengyu (NIH/NHLBI) [E]" <li...@nhlbi.nih.gov<mailto:li...@nhlbi.nih.gov>>
Cc: "gen...@soe.ucsc.edu<mailto:gen...@soe.ucsc.edu>" <gen...@soe.ucsc.edu<mailto:gen...@soe.ucsc.edu>>, 'Jonathan Casper' <jca...@soe.ucsc.edu<mailto:jca...@soe.ucsc.edu>>
Subject: RE: [genome] Finding BAC clones in your browser

Chengyu,

One additional suggestion with respect to finding (human) BAC clones in hg19. As you may know, the RP11 BAC library was created in my lab and can be show on the UCSC hg19 assembly Browser as indicated by Jonathan Casper. We have another human BAC library, which can be uploaded as a custom track (the CHORI-17 “haploid” human BAC library), with insert sizes averaging ~200 kb. The haploid human assembly from the same source DNA is accessible (or will soon be) as a platinum human genome assembly (work at WashU and others). You can upload the CH17 BAC track into the hg19 assembly using the following instructions, from our CHORI-17 library page (https://bacpac.chori.org/library.php?id=231)

How can one find the CHORI-17 BAC clones displayed within the UCSC Browser? Please, first upload (by Copy & Paste) the following links to the UCSC Browser Custom Track Upload<http://genome.ucsc.edu/cgi-bin/hgCustom>: "http://bacpac.chori.org/download/ch17_hg18/ch17.bed" for the hg18 human genome assembly or "http://bacpac.chori.org/download/ch17_hg19/ch17.bed" for the hg19 human genome assembly. After uploading, the CHORI-17 BACs will only be visible for a limited time. So, you may have to repeat this.

Pieter J. de Jong
BACPAC Resources Center (BPRC)
Children’s Hospital Oakland Research Institute (CHORI)


From: Jonathan Casper [mailto:jca...@soe.ucsc.edu]
Sent: Friday, August 01, 2014 5:07 PM
To: Liu, Chengyu (NIH/NHLBI) [E]
Cc: gen...@soe.ucsc.edu<mailto:gen...@soe.ucsc.edu>
Subject: Re: [genome] Finding BAC clones in your browser


Hello Chengyu,

Thank you for your interest in the BAC clones track. We still have a track with BAC end pair data for the GRCh37/hg19 release of the human genome assembly, but we have not yet released a version of that track for the new GRCh38 assembly. We do, however, plan to release that track in the near future. For now, one of our engineers suggests that a work-around is to view the desired BAC in hg19, and use the view in hg38 function to see if it is still there. You can do this by selecting "In Other Genomes (Convert)" option from the "View" menu of the UCSC Genome Browser. Another option is to use the 'Hg38 Diff' track from hg19 to see if the same region is in hg38 or not. Please note that the 'Mapping' set of track controls is collapsed by default on hg19. You will need to expand that set of tracks to be able to turn on the 'Hg38 Diff' track.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu<mailto:gen...@soe.ucsc.edu> or genome...@soe.ucsc.edu<mailto:genome...@soe.ucsc.edu>. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu<mailto:genom...@soe.ucsc.edu>.

--
Jonathan Casper
UCSC Genome Bioinformatics Group

On Tue, Jul 29, 2014 at 10:00 AM, Liu, Chengyu (NIH/NHLBI) [E] <li...@nhlbi.nih.gov<mailto:li...@nhlbi.nih.gov>> wrote:
I am interested in finding BAC clones that span a particular genomic locus. I remember I could simply change a BAC icon from Hide to Full near the bottom of the page, and then all BAC clones will appear in the main window. Now, I could not find the BAC icon. Do you know how can I find BAC clones from your browser?

Thanks,

Chengyu Liu, Ph.D.
National Heart, Lung, and Blood Institute
National Institutes of Health
Tel: 301-435-5-34
--

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