Question: How to edit a google drive URL for upload to ensembl browser?
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gravatar for xavisebastia96
2.2 years ago by
xavisebastia960 wrote:

Hi everyone!

My name is Xavi, I am a bioinformatic working in prostate cancer and I am trying to upload a BAM file to the ensambl browser. I have uploaded first the file to my Google Drive account so as to get an URL to the file. Then I tried putting the URL in the ensambl browser but it is nor valid because the URL has to finish with ".bam". Moreover, it is not possible to upload the BAM file directly since BAM files are too big.

Does anyone know how to edit the Google Drive URL so I could add ".bam" at the end of it? Or does anyone know any other way to upload it such as creating a new URL for the file?

Any help will be useful. Thank you in advance.

browser url ensembl genome • 900 views
ADD COMMENTlink modified 2.2 years ago by Emily_Ensembl19k • written 2.2 years ago by xavisebastia960

Edited your title to make it more specific.

ADD REPLYlink written 2.2 years ago by WouterDeCoster41k

Hi Ben,

Thank you for your helpful answer. You are right, and other problem I had is that the URL that the file first had only could be opened by the server of the company so it didn't worked neither. As you said, it should be figured out uploading the files in the public server so let's see if it works.

Thank you again.

Best wishes

Xavier Sebastià

ADD REPLYlink written 2.2 years ago by xavisebastia960

Hi Xavi,

No problem- very happy to help. Please do let me know how you get on and if you have any other questions.

Best wishes

Ben Ensembl Helpdesk

ADD REPLYlink written 2.2 years ago by Ben_Ensembl1.0k

xavisebastia96 : In future, please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized. This comment should have gone against answer from @Ben.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by genomax72k
2
gravatar for Ben_Ensembl
2.2 years ago by
Ben_Ensembl1.0k
EMBL-EBI
Ben_Ensembl1.0k wrote:

Hi Xavi,

It is not possible to upload custom data to Ensembl via Google Drive. We would advise contacting your IT department, as they are likely to have a public directory (for example FTP) that you can use to store this data and link to Ensembl by providing the URL describing the location and name of the BAM file.

Please note that you will also need to have the the correct indexed file (.BAI) also present in the same directory as the BAM file (although you will not have to provide the URL of the indexed file in the Ensembl Custom Tracks window).

You can read more about adding custom tracks http://www.ensembl.org/info/website/upload/index.html#addtrack http://www.ensembl.org/info/website/upload/large.html

Best wishes

Ben Ensembl Helpdesk

ADD COMMENTlink written 2.2 years ago by Ben_Ensembl1.0k
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