Question: Run Tophat In Galaxy
0
gravatar for Peng, Tao
7.1 years ago by
Peng, Tao170
Peng, Tao170 wrote:
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
rna-seq tophat • 1.8k views
ADD COMMENTlink modified 7.0 years ago • written 7.1 years ago by Peng, Tao170
0
gravatar for Jennifer Hillman Jackson
7.0 years ago by
United States
Jennifer Hillman Jackson25k 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-user@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.cufflinks@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 Subject: run tophat in galaxy Date: Sun, 28 Aug 2011 08:50:04 -0700 To: Jennifer Jackson <jen@bx.psu.edu>, galaxy-user <galaxy-user@lists.bx.psu.edu> 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
ADD COMMENTlink written 7.0 years ago by Jennifer Hillman Jackson25k
===> 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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
ADD REPLYlink written 7.0 years ago by Jennifer Hillman Jackson25k
Hi when I am done with cuffdiff analysis in GALAXY, I got many tabular data output for gene, transcript, promoter and CDS differential expression testing, I wonder if there are some systematic ways to look at the data output from cuffdiff analysis? Thanks, tao
ADD REPLYlink written 7.0 years ago by Peng, Tao170
I wrote a python script and am in the process of writing the xml interface to do just this at this very moment but it uses matplotlib to draw the images. I would be happy to share it with you, but it probably would not work on the public site unless they have matplotlib installed or would be willing to install it. The result is attached and the "error" bars are the 95% confid intervals. File type can be pdf or png (or pretty much anything with small code change). Gus -- In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms. *-Stephen Jay Gould*
ADD REPLYlink written 7.0 years ago by W. Augustine Dunn III10
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 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 select links RefSeq? -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
ADD REPLYlink written 7.0 years ago by Peng, Tao170
0
gravatar for shamsher jagat
7.0 years ago by
United States
shamsher jagat590 wrote:
I have related question If I have to use Ensembl mouse GTF file (Mus_musculus.NCBIM37.64) Do I have to download and reformat it or Galaxy can take it from the source directly? Thanks
ADD COMMENTlink written 7.0 years ago by shamsher jagat590
===> Please use "Reply All" when responding to this email! <=== Hello, Chromosome names will need to be modified once the file is imported, as explained in #5 of the FAQ: http://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faq Hopefully this helps, Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
ADD REPLYlink written 7.0 years ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
7.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:
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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
ADD COMMENTlink written 7.0 years ago by Jennifer Hillman Jackson25k
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 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 use:" mailing Galaxy and to visualize -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
ADD REPLYlink written 7.0 years ago by Peng, Tao170
0
gravatar for Peng, Tao
7.0 years ago by
Peng, Tao170
Peng, Tao170 wrote:
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 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 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 use:" mailing Galaxy and to visualize -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
ADD COMMENTlink written 7.0 years ago by Peng, Tao170
Tao, Cuffdiff output is tabular data, and hence any statistical tool that supports tabular data can be used to analyze/visualize Cuffdiff outputs. In Galaxy, using tools in the categories Statistics and Graph/Display Data should enable you to visualize basic aspects of your data. Good luck, J.
ADD REPLYlink written 7.0 years ago by Jeremy Goecks2.2k
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