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Old 05-13-2010, 07:48 PM   #1
repinementer
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Default Which Genome browser do you use ?

Hi guys I have seen couple of posts discussing about GBs and a nice article from nature about GBs. But still couldn't get the one I can easily access my data with out waiting for hours and hours.

I personally use UCSC GB, It is is awesome browser BUT the server is becoming too slow now a days to upload any file especially high throughput data like RNA-seq files or any other that are in gigabyte sizes.

I would like to know what GB do you use and why you use and why you don't use ?

I want to know which one is the crem dela crem!!
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Old 05-13-2010, 11:16 PM   #2
ffinkernagel
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I have a Gbrowse 2 running here for others to view the data I process,
and while it has taken some time (and learning some more perl than I would have cared for) to get the kinks out, it runs all right for the most part.

In other news, I found none that where 'the crem dela crem' - more of a dilema to choose one, actually.
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Old 05-14-2010, 06:04 AM   #3
mgogol
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UCSC and IGV are my faves.

You may try using BigWig/BigBed files at UCSC to avoid the upload lag.
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Old 05-14-2010, 06:28 AM   #4
qtrinh
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You can also download the UCSC and install it locally on a dedicated server. Loading large data sets will be much faster.

Q
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Old 05-14-2010, 06:36 AM   #5
ffinkernagel
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qtrinh@: Is there a decent way to bootstrap an UCSC now? Last time I looked, the how-to basically started with 'download these 4 terabytes of data from south californa' (... at 150kb/s).
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Old 05-14-2010, 06:51 AM   #6
qtrinh
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Yes, that's what we did (i.e., downloaded the source and followed the build instructions). It's not too bad ...
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Old 05-14-2010, 09:27 AM   #7
ohomann
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Repinementer, for what it is worth, my recently published software, MochiView, might be of use to you. It has been used for desktop visualizion of ChIP-Seq, RNA-Seq, ChIP-Chip, and other data in genomes varying from human to yeast, many of which you can download on the MochiView website. To get a feel for what the software can do, check out the demo videos.
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Old 05-14-2010, 09:30 AM   #8
Auction
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I used IGV from MIT. Tried several local softwares before, only it allow me to upload six WIGs at the same time.
Quote:
Originally Posted by repinementer View Post
Hi guys I have seen couple of posts discussing about GBs and a nice article from nature about GBs. But still couldn't get the one I can easily access my data with out waiting for hours and hours.

I personally use UCSC GB, It is is awesome browser BUT the server is becoming too slow now a days to upload any file especially high throughput data like RNA-seq files or any other that are in gigabyte sizes.

I would like to know what GB do you use and why you use and why you don't use ?

I want to know which one is the crem dela crem!!
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Old 05-14-2010, 09:44 AM   #9
Michael.James.Clark
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Quote:
Originally Posted by ffinkernagel View Post
qtrinh@: Is there a decent way to bootstrap an UCSC now? Last time I looked, the how-to basically started with 'download these 4 terabytes of data from south californa' (... at 150kb/s).
Santa Cruz is in Northern California.

I often use UCSC Genome Browser because I like the instant access to so many tracks, but it can certainly get pretty slow.

You should try out IGV.
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Old 05-14-2010, 07:31 PM   #10
repinementer
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Default Hi Guys

Hi all!
Thanx you for your overwhelming responses. I tried the ones you suggested like IGV and IGB and others. But guys you know they are not so useful (but still can do the job some how).

@Ohomann - Mochiview : Sorry man. I'm certainly not a big fan of commercialised software.

@mgogol: Oh I didn't know that. Thanx for suggestion.

@qtrinh @Clark: Actually that is exactly what I'm thinking! Thanx for suggestion. UCSC is the best.

Have any one tried GeneTrack ? http://code.google.com/p/genetrack/
I haven't seen any one discussing about it?
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Old 05-20-2010, 09:56 AM   #11
ohomann
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Quote:
Originally Posted by repinementer View Post
Hi all!
@Ohomann - Mochiview : Sorry man. I'm certainly not a big fan of commercialised software.
MochiView is not commercial software. It was written in an academic laboratory and is free for use for both academic and corporate users. Source code is available upon request (though it requires agreement to a license that prevents the user from selling the software).
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Old 05-21-2010, 01:35 AM   #12
idonaldson
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I still like to use UCSC GB, but favour using Google Chrome as the web browser, which seems to work faster than the same session on Firefox. I particularly like UCSC because of the 'session' function, which is handy for other bioinformatician types to view the data, plus the easy incorporation of UCSC stored data.

In saying that I like IGV for looking at SNP data.
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