Question: How To View The Tophat Output ?
gravatar for Xu, Jianpeng
6.7 years ago by
Xu, Jianpeng30
Xu, Jianpeng30 wrote:
Hi , I have installed our local galaxy and tried to run some programs. I have run the Tophat with RNA-seq data. There are two output files: accepted_hits, and splice_junctions. Can you tell me how to view the results files? Is there a tool on galaxy that can be used to view the result ? Can I use IGV to view it ? Thanks a lot. Jianpeng ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
galaxy • 1.0k views
ADD COMMENTlink modified 6.7 years ago by Jennifer Hillman Jackson25k • written 6.7 years ago by Xu, Jianpeng30
gravatar for Jennifer Hillman Jackson
6.7 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hello Jianpeng, Please see step #2 in the RNA-seq tutorial for visualization help: For IGV and other external applications, these links will appear inside dataset boxes that have database/datatype identifiers that meet the criteria for the visualization tool (each is different). Instructions for those that require set-up are in these wikis: s%20Tutorial When doing the set up, these will be the areas of the source involved for external application: central/src/c510097f7018/display_applications central/src/c510097f7018/universe_wsgi.ini.sample (modify "# -- Display site" as needed) Loading the data from the RNA-seq tutorial into a history on the main Galaxy server will give you an example of what the links looks like once set up (if you choose to do them all). Thanks, Jen Galaxy team
ADD COMMENTlink written 6.7 years ago by Jennifer Hillman Jackson25k
Just to add, Trackster is pretty awesome for RNA-seq data and well worth learning to use. If you also want to see it in IGV you can load the BAM and "gtf" files, but you will have to download "gtf" files to your local drive, then load them from the file menu. You can view the Bam without downloading by following Jennifer's instructions below.
ADD REPLYlink written 6.7 years ago by Jim Robinson150
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