Question: How To Get "Alternate Gene Name" (Gene_Id) From Ucsc Table Browser?
1
gravatar for Dan D
7.2 years ago by
Dan D6.8k
Tennessee
Dan D6.8k wrote:

On the UCSC graphical genome browser, the "alternate gene names" are shown, like in the picture below:

enter image description here

If I use the Table Browser to get RefSeq genes:

enter image description here

I see that the data I want are in a field that isn't normally retrieved:

enter image description here

Is there a way to get that field, circled in blue, instead of the default field, circled in red, into a BED file from the UCSC table browser?

bed ucsc browser • 3.4k views
ADD COMMENTlink modified 7.2 years ago by Gjain5.3k • written 7.2 years ago by Dan D6.8k

Thanks for three great suggestions! I'm trying them out now!

ADD REPLYlink written 7.2 years ago by Dan D6.8k

Thanks again everyone for the very helpful answers. I learned quite a bit about the table browser by going through them. What I want to do, however, is get a BED file, just like what I would normally get from selecting the "BED" option, except that I want the "name2" values instead of the "name" values. The more I dig around, the more it looks like this isn't possible in a direct fashion.

ADD REPLYlink written 7.2 years ago by Dan D6.8k

what do you mean by direct fashion?

ADD REPLYlink written 7.2 years ago by Gjain5.3k

sorry, let me clarify. Using the method that you suggested, I can indeed retrieve the data I want. However, the columns aren't in proper BED format. Want I ultimately want to do is visualize these genes on Galaxy's Trackster Visualization feature so that it has the same gene labels as the UCSC browser. Now, I could pull these data from the UCSC table browser, reformat them with a perl script, and then re-import them into Galaxy, but I'm trying to see if there's a more direct way of doing so, directly through the table browser.

ADD REPLYlink written 7.2 years ago by Dan D6.8k

Ahh ... i get it now ... and i agree that its not straight forward sometime ... you indeed have to re-process the information to get the desired format for further visualization. Looks like you are on the right track. You can even use excel quickly to rearrange the columns in the bed format.

ADD REPLYlink written 7.2 years ago by Gjain5.3k
5
gravatar for Pierre Lindenbaum
7.2 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum121k wrote:

using the ucsc mysql server:

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19  -N -e 'select chrom,txStart,txEnd,name2,strand from refGene ' 

chr19    20115226    20150277    ZNF682    -
chr17    40274755    40275371    HSPB9    +
chr1    34610    36081    FAM138A    -
chr6_qbl_hap6    2882090    2899191    PRRC2A    +
chr3    10327433    10334631    GHRL    -
chr2    220378891    220403494    ASIC4    +
chr17    18086866    18113267    ALKBH5    +
chr1    1658823    1677438    SLC35E2    -
chr1    700244    714068    LOC100288069    -
chr11    129872518    129875381    LINC00167    +
ADD COMMENTlink written 7.2 years ago by Pierre Lindenbaum121k

Hi, very good...

But how can I do that for USCS Genes instead refseq Genes?

Thank you

ADD REPLYlink written 3.0 years ago by silas008100
4
gravatar for Gjain
7.2 years ago by
Gjain5.3k
Göttingen, Germany
Gjain5.3k wrote:

Hi Deedee,

If you change you selection of output file from "BED browser extensible file" to "Selected field from primary and related tables"and then choosing the fields you want in you output file.

Step 1: Selected field from primary and related tables

image1

Step 2: choosing the fields you want in you output file:

image2

This is the way you can do it from web browser tool. I hope this helps.

ADD COMMENTlink modified 7.2 years ago • written 7.2 years ago by Gjain5.3k
1
gravatar for Sukhdeep Singh
7.2 years ago by
Sukhdeep Singh9.8k
Netherlands
Sukhdeep Singh9.8k wrote:

So, from the 2nd image, in the output format, select the option selected fields from primary and related tables then get output and then from the list, select the name2 checkbox for alternate names and whatever other attributes you want.

List looks like

bin  
name    Name of gene (usually transcript_id from GTF)
chrom   Reference sequence chromosome or scaffold
strand  + or - for strand
txStart Transcription start position
txEnd   Transcription end position
cdsStart    Coding region start
cdsEnd  Coding region end
exonCount   Number of exons
exonStarts  Exon start positions
exonEnds    Exon end positions
score    
name2   Alternate name (e.g. gene_id from GTF)
cdsStartStat    enum('none','unk','incmpl','cmpl')
cdsEndStat  enum('none','unk','incmpl','cmpl')
exonFrames  Exon frame {0,1,2}, or -1 if no frame for exon

Cheers

ADD COMMENTlink modified 7.2 years ago • written 7.2 years ago by Sukhdeep Singh9.8k
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