Browsers/Viewers for RNAseq

[imilne]

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

[gavin.oliver]

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.

[Xi Wang]

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.

[Jim Robinson]

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.

[strob]

http://bioinf.scri.ac.uk/tablet/

seems interesting and works fine (I did some small tests)

[Xi Wang]

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.

[Xi Wang]

Thanks steven,
You gave us great namy of names!

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!

[Jim Robinson]

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

[steven]

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?

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.

[malcook]

Igv

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.

[lcollado]

I haven't used most of the above ones, but you can also use GenomeGraphs with biomaRt inside R / Bioconductor.

Leo

[apratap]

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

[lh3]

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.

[Xi Wang]

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?

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.

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