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Old 01-25-2014, 09:47 PM   #1
bio_informatics
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Default Web based genome browser

I need to work on web browser, web based (not desktop).
I have a list of them:
1) Jbrowse
2) Gbrowse
3) Gaggle
4) IGV
5) ensembl
How do I set the criteria to use these?
I am working on prokaryotic genome. On what features should the final tool be selected?
I read through many of them, almost of them have features of zooming, panning, chip-seq.

Kindly help me.
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Old 01-25-2014, 10:10 PM   #2
maasha
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Jbrowse is now quite mature and the gives the best browsing experience IMHO. But the choice totally depends on what you actually need.
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Old 01-25-2014, 10:17 PM   #3
bio_informatics
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Thank you for reply.
What needs to be taken care while I filter the tools?
file format(s), ease of installation, etc?

I need more insight in this.
I will be installing tool on server without admin rights.

Quote:
Originally Posted by maasha View Post
Jbrowse is now quite mature and the gives the best browsing experience IMHO. But the choice totally depends on what you actually need.
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Old 01-25-2014, 10:20 PM   #4
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Well, you need to find out what exactly you want from the genome browser. Then figure out if it can give you this, and finally, how.
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Old 01-25-2014, 10:22 PM   #5
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You could add Geneious (offline) onto your list.

Personally I like IGV for offline browsing as its fast easy to do without the hassle of setting anything online. While I prefer Gbrowse and Jbrowse for browsing through genes online.

I know the author of Jbrowse wants to introduce some really neat features into Jbrowse in the future and basically replace Gbrowse in terms of its flexibility.
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Old 01-25-2014, 10:30 PM   #6
maasha
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Btw, I posted this question some years ago:

http://www.biostars.org/p/9168/

so also search!
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Old 01-25-2014, 10:35 PM   #7
bio_informatics
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Hi Zapages,
Thank you for offline tool(s). But unfortunately, I cannot count them.
Ohh, great.
I am digging more in Jbrowse.
Quote:
Originally Posted by Zapages View Post
You could add Geneious (offline) onto your list.

Personally I like IGV for offline browsing as its fast easy to do without the hassle of setting anything online. While I prefer Gbrowse and Jbrowse for browsing through genes online.

I know the author of Jbrowse wants to introduce some really neat features into Jbrowse in the future and basically replace Gbrowse in terms of its flexibility.
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Old 01-25-2014, 11:05 PM   #8
bio_informatics
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Thank you for this URL.
Quote:
Originally Posted by maasha View Post
Btw, I posted this question some years ago:
http://www.biostars.org/p/9168/

so also search!
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Old 01-26-2014, 05:23 AM   #9
GenoMax
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One important piece of information that @bio_informatics has omitted to provide is if other users will need access this browser (from the web?).

@bio_informatics does NOT have admin rights on this server so that may eliminate some tools since will require database backends/web servers. Is there a chance that you can work with the system administrators to facilitate that part (which would also give you access to expertise that would be needed for setting up more complex tools). Perhaps you are planning to do that.

IGV may be the simplest choice since this is a prokaryotic genome and IGV should be able to use qualified web links for data files potentially allowing others to access the data remotely. Failing that files can always be downloaded locally and then viewed.

UCSC microbial genome browser could potentially be used (if the genome is available there) with local data as custom tracks.
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Old 02-03-2014, 01:56 AM   #10
bio_informatics
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Thank you for your reply.
Yes, other user(s) shall access this browser.

I had dug more on administrator part, and finally confirmed that there is will be other Database created by the admin.
Access to that database (password, username) will be provided to us. That is it.

I need browser that is more readable to Biologists. Having more functionalities by default won't be good.

After looking to the online versions/examples available, I have narrowed down to JBrowse.
I would like to confirm if JBrowse supports custom tracks.

http://www.gmod.org/wiki/JBrowse
I went through 2013 and 2012 pdf presentations available on this, but I am still not clear if Custom tracks are supported by JBrowse.

Thank you.
Quote:
Originally Posted by GenoMax View Post
One important piece of information that @bio_informatics has omitted to provide is if other users will need access this browser (from the web?).

@bio_informatics does NOT have admin rights on this server so that may eliminate some tools since will require database backends/web servers. Is there a chance that you can work with the system administrators to facilitate that part (which would also give you access to expertise that would be needed for setting up more complex tools). Perhaps you are planning to do that.

IGV may be the simplest choice since this is a prokaryotic genome and IGV should be able to use qualified web links for data files potentially allowing others to access the data remotely. Failing that files can always be downloaded locally and then viewed.

UCSC microbial genome browser could potentially be used (if the genome is available there) with local data as custom tracks.
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Old 02-03-2014, 02:00 AM   #11
maasha
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Jbrowse supports all sorts of custom track types.


Martin
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Old 02-03-2014, 02:02 AM   #12
bio_informatics
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@Martin:
Thanks a lot for your confirmation.
I will go ahead with it.
Quote:
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Jbrowse supports all sorts of custom track types.


Martin
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