Question: link genome browser to locations
0
gravatar for Azhar
10 days ago by
Azhar20
China
Azhar20 wrote:

Hi Hellow every one, I want to link my excel file with genomic locations, with genome browser and also upload in mysql to visualize, I think easy option is to make hyperlink by using http://genome.ucsc.edu/cgi-bin/hgTracks?org=[org]&db=[db]&position=[position] but i dont know how to use this i tired but faced some problems any body know about this and also guide me if my approach is right

next-gen • 151 views
ADD COMMENTlink written 10 days ago by Azhar20

So what was the problem

ADD REPLYlink written 10 days ago by Titus570

i want my location to be as hyper link using a formula using http://genome.ucsc.edu/cgi-bin/hgTracks?org=[org]&db=[db]&position=[position] becuase i have number of locations so i want to make a formula so i click and drag easliy for eg chr3:150000-160000:- i want to make this hyper link

ADD REPLYlink written 9 days ago by Azhar20

Ok so i did it in 2 step :

  1 case were you use concatenate function your values for example for me in case D2 :
=CONCATENATE("https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtposition=chr";A2;"%";B2;"-";C2)

A2 = chromosome value

B2 = position start

C2 = position end

  2 In an other case then you use HYPERLINK to me in case E2 :

=HYPERLINK(D2,"ucsc_link")

Best

ADD REPLYlink modified 9 days ago by genomax40k • written 9 days ago by Titus570

Is a UCSC browser necessary? If not, then just use IGV on your own machine.

If you really want to use UCSC then you will need to create either a CUSTOM TRACK or a TRACK HUB.

From UCSC: "The TRACK HUB utility offers a convenient way to view and share very large sets of data. Individuals wishing to display only a few small data sets may find it easier to use the Genome Browser CUSTOM TRACK utility."

ADD REPLYlink modified 10 days ago • written 10 days ago by kennethcondon20071.1k

Thanks for your answer but my question is different.Regards

ADD REPLYlink modified 9 days ago • written 9 days ago by Azhar20
2

I think you should read my question first .... Do you understand?

Azhar, that is quite rude, and not the way to do conversation on professional / scientific forums. Please phrase your statements to be more polite and professional.

ADD REPLYlink written 9 days ago by Ram13k

Okay I noted thanks

ADD REPLYlink written 9 days ago by Azhar20
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