Which Genome browser do you use ?

repinementer · 05-13-2010, 07:48 PM

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!!

ffinkernagel · 05-13-2010, 11:16 PM

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.

mgogol · 05-14-2010, 06:04 AM

UCSC and IGV are my faves.

You may try using BigWig/BigBed files at UCSC to avoid the upload lag.

qtrinh · 05-14-2010, 06:28 AM

You can also download the UCSC and install it locally on a dedicated server. Loading large data sets will be much faster.

Q

ffinkernagel · 05-14-2010, 06:36 AM

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).

qtrinh · 05-14-2010, 06:51 AM

Yes, that's what we did (i.e., downloaded the source and followed the build instructions). It's not too bad ...

ohomann · 05-14-2010, 09:27 AM

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.

Auction · 05-14-2010, 09:30 AM

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

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!!

Michael.James.Clark · 05-14-2010, 09:44 AM

Quote:

Originally Posted by ffinkernagel

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.

repinementer · 05-14-2010, 07:31 PM

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?

ohomann · 05-20-2010, 09:56 AM

Quote:

Originally Posted by repinementer

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).

idonaldson · 05-21-2010, 01:35 AM

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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05-13-2010, 07:48 PM	#1
repinementer Member Location: asia Join Date: Dec 2009 Posts: 80	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!!

05-14-2010, 07:31 PM	#10
repinementer Member Location: asia Join Date: Dec 2009 Posts: 80	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?

05-13-2010, 11:16 PM	#2
ffinkernagel Senior Member Location: Marburg, Germany Join Date: Oct 2009 Posts: 110	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.

05-14-2010, 06:04 AM	#3
mgogol Senior Member Location: Kansas City Join Date: Mar 2008 Posts: 197	UCSC and IGV are my faves. You may try using BigWig/BigBed files at UCSC to avoid the upload lag.

05-14-2010, 06:28 AM	#4
qtrinh Member Location: Canada Join Date: May 2008 Posts: 20	You can also download the UCSC and install it locally on a dedicated server. Loading large data sets will be much faster. Q

05-14-2010, 06:36 AM	#5
ffinkernagel Senior Member Location: Marburg, Germany Join Date: Oct 2009 Posts: 110	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).

05-14-2010, 06:51 AM	#6
qtrinh Member Location: Canada Join Date: May 2008 Posts: 20	Yes, that's what we did (i.e., downloaded the source and followed the build instructions). It's not too bad ...

05-14-2010, 09:27 AM	#7
ohomann Junior Member Location: San Francisco, CA Join Date: Nov 2009 Posts: 5	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.

05-21-2010, 01:35 AM	#12
idonaldson Member Location: Manchester, UK Join Date: Oct 2009 Posts: 37	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.