Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Tophat Deletions Output
0
gravatar for i b
6.3 years ago by
i b • 330
i b • 330 wrote:
dear all, how can we use the tophat deletions output? e.g. if I want to see and conpare between two samples if a specific gene or transcript had been deleted, how can I use this output? is visualisation enough? thanks, ib
rna-seq tophat • 949 views
ADD COMMENT • link •
modified 6.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.3 years ago by i b • 330
0
gravatar for Jennifer Hillman Jackson
6.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Irene, The file is described in the TopHat manual: http://tophat.cbcb.umd.edu/manual.html#output Along with the insertion files, deletions describes variation between the query and the reference genome at the base level (nucleotide). It does not describe whole transcripts or genes. How to use this information is really up to you. This is very large and popular topic area with more information then I could outline in a simple email reply. Even in Galaxy there are many tools and data sources complete with descriptions and help and links to even more resources. More of these are under active development. The base way to start is with some research: Galaxy searches in the Tool panel, Pages, Workflows, Tool Shed, the Wiki, Galaxy custom google searches or even just a plain Google with keywords like "SNP" or "Variation" or "Indel" or similar, alone or in combination, should get you going, if this interests you. Take care, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org
ADD COMMENT • link written 6.3 years ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 178 users visited in the last hour