Annotation

Question: Annotation

6.7 years ago by

Dear galaxy users, This might be a very basic question to most of you. But I was hopimg I could get better understanding of this concept by asking you all. How exactly can we accomplish annotation of our reads? The combination of Tophat and cufflinks does annotate genes right? . I am a bit confused regarding this topic. Any help will be much appreciated. Thanks.

rna-seq cufflinks • 1.6k views

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modified 6.7 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.7 years ago by hsharm03@students.poly.edu • 20

6.7 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello, The tools TopHat/Cufflinks will map and assemble transcripts from sequencing reads. This mapping give each component (short read, transcript, gene boundary) genomic coordinates with respect to the target reference genome. Annotation is also mapped to the reference genome by genomic coordinates. This can be derived from different sources, a look at a genome browser project that focuses on annotation will help you to understand the concept. Good choices can be found under the Galaxy tool group "Get Data". One way to merge the two (assign "annotation" to a "sequence/transcript/gene"), is to identify overlapping coordinate regions on the reference genome between the two. Please see the tools in the group "Operate on Genomic Intervals" and the associated wiki for help/choices http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations. Galaxy is a good resource for this type of analysis. Another way to obtain annotation is to run annotation algorithms directly on the sequence data itself. This is a large and varied analysis space. The public main Galaxy server has some tools for this type of analysis and more are offered if you decided to run a local/cloud instance with repositories from the Tool Shed. http://getgalaxy.org http://wiki.g2.bx.psu.edu/Tool%20Shed For annotation, it is best to know what you are looking for, perform some searches both within the web tools you prefer and with a search tool such as Galaxy, use that research to determine the best platform to use the tool, then sort out the technical details. For general technical 'how-to-use' help with Galaxy, plus some basic scientific operations, these are good places to get oriented/started: http://wiki.g2.bx.psu.edu/Learn https://main.g2.bx.psu.edu/u/james/p/exercises Best, Jen Galaxy team

ADD COMMENT • link written 6.7 years ago by Jennifer Hillman Jackson ♦ 25k

Hello, I am new in Galaxy and like to analyze a set of CLIP-Seq data (for RNA binding protein, so cDNA is the target). Does anyone here have experience on this and what is the workflow on Galaxy? Thanks in advance! Michael Email Disclaimer: www.stjude.org/emaildisclaimer

ADD REPLY • link written 6.7 years ago by Wang, Michael • 30

Hi Michael, I wanted to reply to this older thread, too. (For those wondering how CLiP-Seq works, I found http://starbase.sysu.edu.cn very helpful). Galaxy does not have any CLiP-Seq specific tools at present, but many of Galaxy's tools would be applicable to any bioinfomatic's workflow. If necessary specialized tools for this particular analysis were added to the Tool Shed (http://toolshed.g2.bx.psu.edu, I didn't see any, yet), these could be added into a local or cloud instance and incorporated right away. You might want to make an inquiry on the galaxy-dev@bx.psu.edu mailing list to see if any developers have your favorite tools planned for Tool Shed submission. Other galaxy-users are still welcome to add to this thread! Best, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org

ADD REPLY • link written 6.6 years ago by Jennifer Hillman Jackson ♦ 25k

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