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  • 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
    Last edited by Xi Wang; 08-08-2010, 11:42 PM.
    Xi Wang

  • #2
    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, 07:47 AM.

    Comment


    • #3
      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

      Comment


      • #4
        I haven't used most of the above ones, but you can also use GenomeGraphs with biomaRt inside R / Bioconductor.

        Leo
        L. Collado Torres, Ph.D. student in Biostatistics.

        Comment


        • #5
          Igv

          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.

          Comment


          • #6
            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.

            Comment


            • #7
              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

              If you are unable to find something or have a question about our new website, please email [email protected]. For other inquiries related to the Broad Institute, the necessary contact information can be found here.


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

              If you are unable to find something or have a question about our new website, please email [email protected]. For other inquiries related to the Broad Institute, the necessary contact information can be found here.


              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

              Comment


              • #8
                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!
                Xi Wang

                Comment


                • #9
                  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.
                  Xi Wang

                  Comment


                  • #10


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

                    Comment


                    • #11
                      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.

                      Comment


                      • #12
                        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.
                        Xi Wang

                        Comment


                        • #13
                          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.

                          Comment


                          • #14
                            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
                            Our software: Tablet | Flapjack | Strudel | CurlyWhirly | TOPALi

                            Comment


                            • #15
                              @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, 07:51 AM.

                              Comment

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