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link genome browser to locations

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
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written by Azhar • Azhar

So what was the problem

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written by Titus Titus

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

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written by Azhar • Azhar

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

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updated by GenoMax GenoMax • written by Titus Titus

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."

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written by BioinfGuru BioinfGuru

Thanks for your answer but my question is different.Regards

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written by Azhar • Azhar

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.

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written by Ram Ram

Okay I noted thanks

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written by Azhar • Azhar

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