Hi I wonder how I can quantitatively visualize expression of a gene/transcript which has a significant p-value/q value from splicing differential testing from Cuffdiff analysis? I tried track browser in GALAXY and UCSC genome browser and none of them really provide a quantitative analysis of gene/transcript expression from Cuffdiff results.
Thanks, tao -----Original Message----- From: Peng, Tao Sent: Friday, September 30, 2011 3:13 PM To: 'Jennifer Jackson' Cc: galaxy-user Subject: RE: [galaxy-user] run tophat in galaxy Thanks a lot. Please see the attached screen shot from using Browser in GALAXY for viewing results of Tophat. What do those numbers mean? Is there any way to adjust Y-axis to have the bar taller so it will be easier to see? Thanks, tao -----Original Message----- From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Tuesday, September 27, 2011 1:13 PM To: Peng, Tao Cc: galaxy-user Subject: Re: [galaxy-user] run tophat in galaxy Hi Tao, Yes, the resulting SAM dataset can be converted to BAM and viewed in the GTB (Galaxy Track Browser). http://galaxyproject.org/wiki/Learn -> scroll to "Visualization" to find: http://galaxyproject.org/wiki/Learn/Visualization The GTB can be reached through a different links, but one quick way to do this is: 1 - start with TopHat's output SAM dataset 2 - use the tool "NGS: SAM Tools -> SAM-to-BAM" 3 - hover over "Visualization" in the top menu bar then click on "New Track Browser" 4 - at the prompt, name the visualization and specify the reference genome and click on "Continue" 5 - once the browser opens, click on the "Add Datasets to Visualization" prompt to add datasets. Histories and Libraries can be navigated, selected, then individual datasets selected and loaded. 6 - default view for BAM datasets a coverage histogram. 7 - adding more tracks and other functions can be performed by using the left menu "Actions" on the GTB interface. Be sure to use "Save" before navigating away if you want to use the same browser again. If datasets are not available to add to a browser, then likely there is a mismatch between the browser's reference database and the database assigned to the dataset. In some cases this can and should be adjusted (perhaps database was unassigned after an analysis). The SAM file can also be converted to interval, then BED format for visualization, but BAM is the most direct route and preserves the sequence content when zoomed in at the base level. Hopefully this helps you and others to learn more about the GTB. This tool is under active development. Screencasts and more example documentation is on the way soon to offer more help. Best, Jen Galaxy team On 9/27/11 12:45 PM, Peng, Tao wrote: > Jen, thank you for following up on my question. > Is any tool in GALAXY to visualize the coverage of aligned reads from > TopHat on human chromosomes (histogram or density plot)? > > Tao > > -----Original Message----- > From: Jennifer Jackson [mailto:j...@bx.psu.edu] > Sent: Thursday, September 15, 2011 2:37 PM > To: galaxy-user > Cc: Peng, Tao > Subject: Re: [galaxy-user] run tophat in galaxy > > ===> Please use "Reply All" when responding to this email!<=== > > Hi Tao, > > I made an error in my prior reply, it is possible to guide assembly in > TopHat. To do this, on the TopHat form, change "TopHat settings to use:" > > from "Use Defaults" to "Full parameter list". In the expanded form: > > 1 - change "Use Own Junctions:" to be "yes". > 2 - change "Use Gene Annotation Model:" to be "yes" > 3 - in the new pull-down menu, select the GTF file from your history > > Great question! Glad that we were able to provide you with the correct > instruction, > > Best, > > Jen > Galaxy team > > On 9/15/11 1:38 PM, Jennifer Jackson wrote: >> ===> Please use "Reply All" when responding to this email!<=== >> >> Hello Tao, >> >> Sorry for the delayed reply, your question did not post to the mailing >> list since the "to" was not _only_ to galaxy-user. >> >> Going forward, please leave off any "to" or "cc" to team members when >> asking a question. Send all questions directly "to" >> "galaxy-u...@bx.psu.edu" and do not include any "Re" or "Fwd" text in >> the subject line. >> >> Regarding RNA-seq analysis and reference GTF files, the place to >> incorporate the GTF file is in the Cufflinks step, the option to > select >> the GTF file from your history is on the tool's form. If you have >> questions about the tools that are not addressed by these help links: >> >> http://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faq >> http://usegalaxy.org/u/jeremy/p/galaxy-rna-seq-analysis-exercise >> >> then contacting the tool authors would be the next step: >> email tophat.cuffli...@gmail.com >> >> To visualize the data, the available options will be links associated >> with each dataset (expand the dataset box to locate these). The Galaxy >> Track Browser (GTB) aka "Trackster", UCSC Genome Browser, Ensembl, and >> GeneTrack are potential options; the datatype will determine which > links >> are provided. >> >> Hopefully this helps, >> >> Best, >> >> Jen >> Galaxy team >> >> >> -------- Original Message -------- >> Subject: run tophat in galaxy >> Date: Sun, 28 Aug 2011 08:50:04 -0700 >> From: Peng, Tao<tp...@fhcrc.org> >> To: Jennifer Jackson<j...@bx.psu.edu>, galaxy-user >> <email@example.com> >> >> >> >> Hi how can I specify a GTF gene annotation file when running tophat to >> guide the alignment to human genome? What is the best way to visualize >> the tophat results in the context of annotated human genome, i.e. > RefSeq? >> >> Thanks, >> >> tao >> >> >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org. Please keep all replies on the list by >> using "reply all" in your mail client. For discussion of >> local Galaxy instances and the Galaxy source code, please >> use the Galaxy Development list: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >> http://lists.bx.psu.edu/ > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/