UCSC

[Vaneet Lotay]

Hello,

 

I was trying to download a track off of the UCSC genome browser and realized it isn’t as simple as right-clicking on the track and saving the BED file, at least not that I could notice.

 

I was trying to download the BED file for the Xenopus Laevis v2 genome, specifically the RefSeq track as it has gene symbols for many genes.

 

I began to use Table Browser to download that specific BED and selected the refGene table but it gave me a BED file with not gene symbols for names, only accession IDs I believe:

 

chr1L     48194411             48236602             NM_001092627 0              -              48195734             48211573             0              12                1476,141,71,169,168,104,724,181,152,238,179,55,                0,2281,4072,5668,5919,7356,10074,10938,11680,16235,17028,42136,

chr1L     59764196             59771655             NM_001096243 0              +             59764272             59771332             0              8                235,250,107,224,205,114,134,378,             0,1715,2105,4214,5345,5719,6777,7081,

chr1L     66051650             66070304             NM_001096055 0              +             66051685             66062965             0              13                99,65,45,54,120,87,127,13,115,86,70,40,166,                0,3600,4589,6999,7984,8541,10523,11263,11276,12194,15429,15827,18488,

chr1L     77587341             77613672             NM_001087183 0              +             77587477             77613249             0              6                194,152,45,110,883,558, 0,7497,13580,21694,22965,25773,

chr1L     89120318             89139188             NM_001280624 0              +             89137176             89138851             0              4                72,89,254,778,   0,1515,16850,18092,

 

Is there any way I can download the BED file but with the actual gene symbols that were shown in the genome browser?

 

Thanks,

 

Vaneet

 

Vaneet Lotay

Xenbase Bioinformatician

716 ICT Building - University of Calgary

2500 University Drive NW

Calgary AB T2N 1N4

CANADA

 

[Cath Tyner]

Hi Vaneet! 

Thanks for contacting the UCSC Genome Browser support team! Absolutely, you can use the Table Browser to add related tables and columns to your query, thus including the gene symbols in your output. Here is a section, "Get gene symbols in a query" from the Table Browser User Guide which shows those steps, but if you have any additional questions, please let us know!

Please respond to this list if you have further questions, and please always feel free to search our mailing list archives for related posts.

Thank you for contacting the UCSC Genome Browser support team. 

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. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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