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Old 02-03-2010, 07:59 PM   #1
Xi Wang
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Default Browsers/Viewers for RNAseq

Hello everyone!

I am here collecting the information of browsers/viewers especially for RNA sequencing data, which can mainly show the gene annotation track, read track (including spliced reads), and some other annotation tracks. This is the basic requirment of RNA-seq data viewing.

Thanks to the Seqanswers wiki page, I listed the browsers/viewers for RNA-seq below. But due to my limited experience, the list is not full. Anyone helps to complete this list is appreciated. Also, the unique feature for each browser/viewer is important, as users can choose their own browser/viewer accordingly. Could please help me to fill them too?

Code:
Lookseq
MochiView
SeqMonk
IGV
MagicViewer
SAMtools
UCSC genome browser
GenomeGraphs
Thanks in advance for your time and your attention!

EDIT: I have collected some browsers applicable for RNA-seq. It seems too few due to the requirement of gene annotation tracks.
Code:
Software            Author Affiliation      Supported_format                                          Remote    Unique_feature                                             Link  
IGV                 Broad Institute         TDF,CN,SNP,GCT,RES,GFF/GFF3,BED,SAM/BAM,WIG,TAB,IGV...    Yes       supports a wide variety of data types and format           http://www.broadinstitute.org/igv/
IGB                 UNC Charlotte           BAM,BED,PSL,...							animated zooming, highly configurable,..                   http://www.bioviz.org/igb
UCSC Browser        UCSC                    BED,bigBed,BEDGRAPH,GFF,GTF,WIG,bigWig,MAF,BAM,PSL        Yes       various of annotation tracks, Working with table browser   http://genome.ucsc.edu/   
CisGenome Browser   Stanford                BAR,BED,refFlat,FA,...                                              fold intron, show UCSC tracks                              http://biogibbs.stanford.edu/~jiangh/browser/  
MochiView           UCSF                    Wig,Bed,GFF,FASTA,MEME                                              joint analysis of ChIP-seq and RNA-seq data                http://johnsonlab.ucsf.edu/sj/mochiview-start/ 
SeqMonk             The Babraham Institute  ELAND,GFF,BED,MAQ,SAM                                               nice plot, data filter                                     http://www.bioinformatics.bbsrc.ac.uk/projects/seqmonk/   
Gambit              Boston College          BAM,BED,GFF2,GFF3,FASTA,VCF                                         plugin-aware                                               http://code.google.com/p/gambit-viewer/   
GenomeGraphs        Lawrence Berkeley       Expression data,Annotation tracks                                   Bioconductor package                                       http://bioconductor.org/packages/release/bioc/html/GenomeGraphs.html  
GenomeView
BamView+artemis

"Remote" means viewing alignment over HTTP/FTP
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Last edited by Xi Wang; 08-09-2010 at 12:42 AM.
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Old 02-03-2010, 09:58 PM   #2
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Vote for IGV.

EDIT: One minor issue is IGV does not display inserted sequences. You will not easily know how inserted sequence may mess the alignment, which sometimes is important to me. Jim is planning to add this feature. In addition, sometimes the alignment is sitting on a remote file system and transferring a graphical interface over network is slow and inconvenience. In these two cases, I use samtools.

Last edited by lh3; 02-04-2010 at 07:47 AM.
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Old 02-04-2010, 06:20 AM   #3
apratap
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Hi All

I haven't tried everything on the list here but from my experience I like IGV. I am still trying to work out a solution where I could integrate the browser into webpage. I think it may not happen at all and the best I could do is to get a link which could start the jnlp for user.

Any suggestions ?

-A
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Old 02-04-2010, 07:08 AM   #4
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I haven't used most of the above ones, but you can also use GenomeGraphs with biomaRt inside R / Bioconductor.

Leo
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Old 02-04-2010, 07:36 AM   #5
malcook
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Default Igv

Quote:
Originally Posted by apratap View Post
Hi All

I haven't tried everything on the list here but from my experience I like IGV. I am still trying to work out a solution where I could integrate the browser into webpage. I think it may not happen at all and the best I could do is to get a link which could start the jnlp for user.

Any suggestions ?

-A
IGV architect/developer Jim Robinson told me that he might implement a URL API for navigating the browser, in addition to existing method of listening for navigation commands on a port. I will point this thread out to him as evidence of additional interest in this feature.

BTW - I also use IGV to great satisfaction and recommend it.
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Old 02-04-2010, 10:10 AM   #6
steven
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Quote:
Originally Posted by Xi Wang View Post
Hello everyone!

I am here collecting the information of browsers/viewers especially for RNA sequencing data, which can mainly show the gene annotation track, read track (including spliced reads), and some other annotation tracks. This is the basic requirment of RNA-seq data viewing.

Thanks to the Seqanswers wiki page, I listed the browsers/viewers for RNA-seq below. But due to my limited experience, the list is not full. Anyone helps to complete this list is appreciated. Also, the unique feature for each browser/viewer is important, as users can choose their own browser/viewer accordingly. Could please help me to fill them too?

Code:
Lookseq
MochiView
SeqMonk
IGV
MagicViewer
SAMtools
UCSC genome browser
GenomeGraphs              R/Bioconductor
Thanks in advance for your time and your attention!
Good idea!
Are these ones relevant/useful for RNA-seq?

GBrowse
JBrowse
Madas
IGB
Artemis
EagleView
MapView
NGSview
Tablet

cheers,
s.
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Old 02-04-2010, 10:58 AM   #7
Jim Robinson
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Default RE IGV in Web Page

Hi,

Sorry I missed this thread when it happened, Malcolm just pointed it out to me. Its true you can't embed IGV in a webpage, this could be possible as an applet with a little coding. However, you can create weblinks that will launch IGV as an application with a session you define preloaded. Details are below

http://www.broadinstitute.org/igv/ControlIGV

The link is somewhat ugly, but functional. They look like this

http://www.broadinstitute.org/igv/dy...me&locus=locus

People on this forum are probably interested in the details, the above passes its parameters to a servlet, which generates a custom jnlp file which in turn passes the parameters to the application. Its the only way I know of to pass parameters with jnlp.

Jim
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Old 02-05-2010, 12:00 AM   #8
Xi Wang
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Thanks steven,
You gave us great namy of names!

Quote:
Are these ones relevant/useful for RNA-seq?

GBrowse
JBrowse
Madas
IGB
Artemis
EagleView
MapView
NGSview
Tablet
Has someone used the listed above? What is the unique feature of each? Any reply is appreciated!
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Old 02-05-2010, 01:59 AM   #9
Xi Wang
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Quote:
Originally Posted by lh3 View Post
Vote for IGV.

EDIT: One minor issue is IGV does not display inserted sequences. You will not easily know how inserted sequence may mess the alignment, which sometimes is important to me. Jim is planning to add this feature. In addition, sometimes the alignment is sitting on a remote file system and transferring a graphical interface over network is slow and inconvenience. In these two cases, I use samtools.
Thanks, lh3.
Is what you meant by "inserted sequence" the indels or the introns that have been spliced for mature RNA?
For how IGV works, we also have a question that, is the annotations for the genome getting from the remote server? So you said transferring over network.
Thanks.
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Old 02-05-2010, 02:13 AM   #10
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http://bioinf.scri.ac.uk/tablet/

seems interesting and works fine (I did some small tests)
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Old 02-05-2010, 04:37 AM   #11
Jim Robinson
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Quote:
Originally Posted by Xi Wang View Post
Thanks, lh3.
Is what you meant by "inserted sequence" the indels or the introns that have been spliced for mature RNA?
For how IGV works, we also have a question that, is the annotations for the genome getting from the remote server? So you said transferring over network.
Thanks.
As for the indels, IGV display deletions reasonably, but insertions are denoted by painting a vertical bar at the position of the insertion. In other words the reference remains fixed, it does not "stretch" to accommodated. The inserted bases. This will be fixed in the near future.

Data for the hosted reference assemblies, annotations and sequence, are transferred from a remote server. You can also import your own local server. Originally IGV would not start up the first time if it could not reach our server, that has been fixed.

I am currently moving all of our hosted data, with the exception of very large files like the 1KG BAMS, to the Amazon "cloud". This should make downloads quite fast anywhere in the world. Some testing from users in Europe have been encouraging. I'm looking for volunteers in Asia and Australia to run some tests, please reply if you are able and interested.
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Old 02-05-2010, 05:16 AM   #12
Xi Wang
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Sure Jim, I can help you do the test. Thank you for your effort to provide us such wonderful tool.
You can email me for more details.
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Old 02-05-2010, 05:43 AM   #13
gavin.oliver
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Quote:
Originally Posted by Xi Wang View Post
Thanks steven,
You gave us great namy of names!



Has someone used the listed above? What is the unique feature of each? Any reply is appreciated!
This would indeed be useful info to have.
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Old 02-05-2010, 07:38 AM   #14
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Quote:
Originally Posted by strob View Post
http://bioinf.scri.ac.uk/tablet/

seems interesting and works fine (I did some small tests)
Tablet doesn't have support for gene annotation tracks yet though (which seems to be a requirement of the original poster). It's something we're likely to be adding in the near future if we can decided what level of support to actually include. We don't want to go about creating an entire genome browser just for drawing a few annotation tracks, but also don't want it to be too feature (no pun intended) limited.

I'd be interested to hear opinions on what people would like (either here, or by contacting us via the option in Tablet itself).

I'll also quickly add that for some reason known only to our IT department, all our servers will be powered down and offline for this weekend, so anyone trying to download Tablet between now and Monday is out of luck I'm afraid
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Old 02-05-2010, 07:42 AM   #15
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@Xi Wang

By "inserted sequence" I mean a few bp short insertion. It matters more for SNP calling, but is probably less relevant to RNA-seq.

You can load to IGV an annotation file on your local computer. The efficiency over network is another issue. Suppose I am sitting in US and want to have a look a huge alignment sitting on a Chinese NFS file server. I can only launch IGV from the Chinese server and then the GUI is transferred over X11 to US. Frequently you will find the responsiveness of the interface is bad due to the limited network bandwidth. A terminal viewer like samtools is much faster. Nonetheless, I guess few people share my this concern.

By the way, here is the list of viewers with native support of BAM ("remote" means viewing alignment over HTTP/FTP):

artemis (with bamview plugin)
bamview
gambit
gbrowse (web)
igv (remote)
lookseq (web)
magicviewer
samtools (remote, not supporting annotation)
UCSC browser (web, remote)

Viewers natively supporting BAM are all able to work with huge alignments. The following viewers are able to convert SAM/BAM to their native format. They also work with huge alignment:

gap5
tablet

I am not familiar with the rest, but some certainly have problem with displaying large alignment (e.g. eagleview).

In general, IGV is most matured and easy to use. Samtools may be friendly for some command-line guru, but certainly not useful to RNA-seq as it does not support annotations. You need to do a bit configuration to get lookseq and gbrowse working. But once you set it up, you can host your alignment from your web server and let others have a look. Gambit and magicviewer are under active development. UCSC browser provides another way to host your alignment at UCSC, but I have not tried.

Last edited by lh3; 02-05-2010 at 07:51 AM.
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Old 02-05-2010, 07:46 AM   #16
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Quote:
Originally Posted by lh3 View Post
Viewers natively supporting BAM are all able to work with huge alignments. The following viewers are able to convert SAM/BAM to their native format. They also work with huge alignment:

gap5
tablet
Tablet can read SAM files at the moment, and the version due for release next week will work with BAM too, although it's just an experimental version that parses the file in the same way we handle all formats, so in the short-term you'd still need to read *all* the file. Not good for multi GB files. We will be implementing support for indexed BAM reading though - I think we can manage to make Tablet handle it (and save a ton of memory too) without losing the ability to read all the other formats too.
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Old 02-05-2010, 08:49 AM   #17
Xi Wang
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Quote:
Originally Posted by imilne View Post
I'll also quickly add that for some reason known only to our IT department, all our servers will be powered down and offline for this weekend, so anyone trying to download Tablet between now and Monday is out of luck I'm afraid
Yes, I can get to Tablet website hours ago, but can't now :-(

Quote:
Tablet can read SAM files at the moment, and the version due for release next week will work with BAM too, although it's just an experimental version that parses the file in the same way we handle all formats, so in the short-term you'd still need to read *all* the file. Not good for multi GB files. We will be implementing support for indexed BAM reading though - I think we can manage to make Tablet handle it (and save a ton of memory too) without losing the ability to read all the other formats too.
I like the feature to read SAM/BAM files. It is admitted that SAM is the standard format for sequence/read alignment/mapping, so all browsers/viewers for NGS data should support this format. BAM could be more efficient for large number of reads.

If you have time to add the annotation tracks to Tablet, I am sure that it would have more applications.

Anyhow, thanks for providing your tool!
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Old 02-05-2010, 09:03 AM   #18
Xi Wang
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Quote:
Originally Posted by lh3 View Post
@Xi Wang
You can load to IGV an annotation file on your local computer. The efficiency over network is another issue. Suppose I am sitting in US and want to have a look a huge alignment sitting on a Chinese NFS file server. I can only launch IGV from the Chinese server and then the GUI is transferred over X11 to US. Frequently you will find the responsiveness of the interface is bad due to the limited network bandwidth. A terminal viewer like samtools is much faster. Nonetheless, I guess few people share my this concern.
Yes, we also have this concern. Our group has such project to develop a local browser as well, but still on the way Moreover, the network in China is much poorer, so the local viewer is more needed.

Quote:
By the way, here is the list of viewers with native support of BAM ("remote" means viewing alignment over HTTP/FTP):

artemis (with bamview plugin)
bamview
gambit
gbrowse (web)
igv (remote)
lookseq (web)
magicviewer
samtools (remote, not supporting annotation)
UCSC browser (web, remote)

Viewers natively supporting BAM are all able to work with huge alignments. The following viewers are able to convert SAM/BAM to their native format. They also work with huge alignment:

gap5
tablet
Great. I just had the idea this afternoon that to list/sort the most important features of these browsers/viewers. Such as supporting SAM. Another feature whether a browser/viewer needs network connection to get annotation tracks is also important.

Quote:
I am not familiar with the rest, but some certainly have problem with displaying large alignment (e.g. eagleview).

In general, IGV is most matured and easy to use. Samtools may be friendly for some command-line guru, but certainly not useful to RNA-seq as it does not support annotations. You need to do a bit configuration to get lookseq and gbrowse working. But once you set it up, you can host your alignment from your web server and let others have a look. Gambit and magicviewer are under active development. UCSC browser provides another way to host your alignment at UCSC, but I have not tried.
Thank you very much for the info. You are really appreciated.
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Old 02-05-2010, 09:06 AM   #19
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Default UCSC v IGV

I've tried IGV, and I use it sometimes, but for me UCSC is still pretty compelling.

1) I like the way the figures it generates look
2) You can see stuff better when you're zoomed way out
3) Easy access to all those nice public data annotation tracks
4) Galaxy/Table browser
5) Non-bioinformatician friendly, easy to send a link that loads custom data
6) I can shove a whole bunch of data in it and go trolling around without having any problems, but for me IGV gets kind of slow. Maybe I'm doing something wrong.

This is probably more of a personal preference kind of situation...

I've tried some of those other ones, IGB, gbrowse, GenomeGraphs, but found them lacking in some way or another.
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Old 02-16-2010, 01:40 AM   #20
Xi Wang
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FYI, I have updated the first post in the thread. I just list some browsers applicable for RNA-seq data viewing. Any suggestion is appreciated in case I lost something important. And also any comment is welcome.
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