Hello,
We have been trying to determine a method to convert ChIP-Seq coordinates into a list of genes and are wondering the best way to utilize the Galaxy browser. The UCSC folks suggested you could help but I should have been more specific with my request. Ideally we would like to take global binding coordinates and find out what genes are nearby (ie at either a 1 or 5kb) instead of simply the "closest feature". Might you be able to advise on this? I have enclosed the text (.bed format) file I used to get the binding sites in the UCSC genome browser. Thanks in advance!
Cheers,
Dana
From: Mary Goldman [mailto:mary@soe.ucsc.edu] Sent: Thursday, August 12, 2010 2:06 PM To: Das, Satyabrata Cc: genome@soe.ucsc.edu Subject: Re: [Genome] Genome-wide dataset of protein location conversion
Hi Satya,
If you are looking for the nearest gene to a genomic coordinate, you should use Galaxy ( http://main.g2.bx.psu.edu/). Load your coordinates as a custom track on the UCSC genome browser, go to the table browser and send the output to Galaxy (click the check box after the output option pull down menu). I believe the tool you want is "Fetch closest feature" under the "Operate on Genomic Intervals" menu. If you have questions about Galaxy, please contact their help desk at galaxy-user@lists.bx.psu.edu.
I hope this information addresses your question and is helpful. Please feel free to contact the mail list again if you require further assistance.
Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group
On 8/11/10 10:03 PM, Das, Satyabrata wrote:
Hello,
I am analyzing a genome-wide dataset of protein location coordinates in the following format and want to know if they can be converted to the gene that they are most closely located next to:
chr1:3002834-3002851 chr1:4132776-4132783 chr1:4322743-4322748 chr2:155204062-155204080 chr2:155207569-155207570 chr2:155209754-155209758 chr2:155275773-155275774 chr2:155311478-155311484
The coordinates are derived from the mm8, Feb 2006, Build 36 genome build. I would like to know if the UCSC table browser has a batch function that enables conversion of these coordinates into the gene descriptions or gene symbols that the binding sites are positioned near (either within the gene bodies or intergenically).
Thank you, Satya
Hi Satya, Hi Dana
Another tool and methodology of your interest for chip seq experiments could be, http://great.stanford.edu/ (Genomic Regions Enrichment of Annotations Tool)
They take input as chip seq experiments and i know are integerated with galaxy and UCSC genome browser
Best
Abhay Bioinformatician Eye Diseases: from genetics & Epigenetics to therapy Department of Cell therapy and Regenerative Medicine CABIMER(Andalusian Center of Molecular Biology and regenerative medicine) Sevilla Spain
On 26 August 2010 00:26, Levasseur, Dana dana-levasseur@uiowa.edu wrote:
Hello,
We have been trying to determine a method to convert ChIP-Seq coordinates into a list of genes and are wondering the best way to utilize the Galaxy browser. The UCSC folks suggested you could help but I should have been more specific with my request. Ideally we would like to take global binding coordinates and find out what genes are *nearby* (ie at either a 1 or 5kb) instead of simply the “closest feature”. Might you be able to advise on this? I have enclosed the text (.bed format) file I used to get the binding sites in the UCSC genome browser. Thanks in advance!
Cheers,
Dana
*From:* Mary Goldman [mailto:mary@soe.ucsc.edu] *Sent:* Thursday, August 12, 2010 2:06 PM *To:* Das, Satyabrata *Cc:* genome@soe.ucsc.edu *Subject:* Re: [Genome] Genome-wide dataset of protein location conversion
Hi Satya,
If you are looking for the nearest gene to a genomic coordinate, you should use Galaxy ( http://main.g2.bx.psu.edu/). Load your coordinates as a custom track on the UCSC genome browser, go to the table browser and send the output to Galaxy (click the check box after the output option pull down menu). I believe the tool you want is "Fetch closest feature" under the "Operate on Genomic Intervals" menu. If you have questions about Galaxy, please contact their help desk at galaxy-user@lists.bx.psu.edu.
I hope this information addresses your question and is helpful. Please feel free to contact the mail list again if you require further assistance.
Best, Mary
Mary Goldman UCSC Bioinformatics Group
On 8/11/10 10:03 PM, Das, Satyabrata wrote:
Hello,
I am analyzing a genome-wide dataset of protein location coordinates in the following format and want to know if they can be converted to the gene that they are most closely located next to:
chr1:3002834-3002851
chr1:4132776-4132783
chr1:4322743-4322748
chr2:155204062-155204080
chr2:155207569-155207570
chr2:155209754-155209758
chr2:155275773-155275774
chr2:155311478-155311484
The coordinates are derived from the mm8, Feb 2006, Build 36 genome build. I would like to know if the UCSC table browser has a batch function that enables conversion of these coordinates into the gene descriptions or gene symbols that the binding sites are positioned near (either within the gene bodies or intergenically).
Thank you,
Satya
galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Good Afternoon Dana:
You could produce such a list from a given position with a MySQL operation to the UCSC public MySQL server. Note this Wiki page with a description of the command:
http://genomewiki.ucsc.edu/index.php/Finding_nearby_genes
--Hiram
----- Original Message ----- From: "Dana Levasseur" dana-levasseur@uiowa.edu To: galaxy-user@lists.bx.psu.edu Sent: Wednesday, August 25, 2010 3:26:28 PM GMT -08:00 US/Canada Pacific Subject: [galaxy-user] FW: [Genome] Genome-wide dataset of protein location conversion
Hello,
We have been trying to determine a method to convert ChIP-Seq coordinates into a list of genes and are wondering the best way to utilize the Galaxy browser. The UCSC folks suggested you could help but I should have been more specific with my request. Ideally we would like to take global binding coordinates and find out what genes are nearby (ie at either a 1 or 5kb) instead of simply the “closest feature”. Might you be able to advise on this? I have enclosed the text (.bed format) file I used to get the binding sites in the UCSC genome browser. Thanks in advance!
Cheers,
Dana
galaxy-user@lists.galaxyproject.org
-
Abhay Krishna -
Hiram Clawson -
Levasseur, Dana