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, Taotp...@fhcrc.org To: Jennifer Jacksonj...@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 ___ The Galaxy User list should be used
Re: [galaxy-user] run tophat in galaxy
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 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 ___ 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/
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, Taotp...@fhcrc.org To: Jennifer Jacksonj...@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 ___ 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
Re: [galaxy-user] run tophat in galaxy
=== 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 On 9/15/11 8:22 PM, shamsher jagat 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 On Sun, Aug 28, 2011 at 8:50 AM, Peng, Tao tp...@fhcrc.org mailto:tp...@fhcrc.org wrote: === Please use Reply All when responding to this email! === __ 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 http://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/
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 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 ___ 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/
Re: [galaxy-user] run tophat in galaxy
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 On Sun, Aug 28, 2011 at 8:50 AM, Peng, Tao tp...@fhcrc.org wrote: === Please use Reply All when responding to this email! === ** 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/ ___ 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/
