How To View The Tophat Output ?

Question: How To View The Tophat Output ?

6.7 years ago by

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 COMMENT • link •

modified 6.7 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.7 years ago by Xu, Jianpeng • 30

6.7 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Jianpeng, Please see step #2 in the RNA-seq tutorial for visualization help: https://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise 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: http://wiki.g2.bx.psu.edu/Admin/Tools/External%20Display%20Application s%20Tutorial http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy When doing the set up, these will be the areas of the source involved for external application: https://bitbucket.org/galaxy/galaxy- central/src/c510097f7018/display_applications https://bitbucket.org/galaxy/galaxy- 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 COMMENT • link written 6.7 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 6.7 years ago by Jim Robinson • 150

Similar posts • Search »