How to trancriptome annotations from various tools

4.3 years ago by

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If you mean that you have constructed multiple annotated transcriptomes (assemblies of sorts), and wish to compare, then this can be done many ways. The tools in the groups Extract Features, Operate on Genomic Intervals, and BEDTools should get you started. Seach by your datatype to locate all tools available for each - the description and help will aid you in knowing what operation is performed. And of course comparing to any known annotation will be helpful.

In the end, actually taking a look at the data would be a good idea. Visualizing in a browser both together (perhaps examine a gene bound that has been characterized) and along with other annotation types and maybe some of the comparison datasets. All of these choices may not be available for all genomes, but are for many, and there are techniques to map annotation (RefSeq, Ensemble) across species, to aid in gene bound/transcript elucidation (BLAT, Blast+, etc - can be used in a local/cloud Galaxy).

Perhaps our community will also contribute more ideas. I'll assumed you have already reviewed available advice on http://biostars.org, http://seqanswers.com, etc, .. but if not, these are great resources.

Good luck, and if your question has been misunderstood, please provide more details.

Jen, Galaxy

ADD COMMENT • link written 4.3 years ago by Jennifer Hillman Jackson ♦ 25k

hi mam I want to compare the annotations may be like the GO annotations For the same transcritome I have got different annotations how to normalise it ?

ADD REPLY • link written 4.3 years ago by lakshmikrish.friends • 0

Hi again, I understand your question better now.

Some tools that gather up annotations like GO can gather up too much (linking in loose connections) or too little (focus on a specific functional/relationship area). Others may be just right. Knowing how each is pulling in the information should help you to decide whether it is useful for you. Automated annotations can be good leads for discovery, but curated annotations will be more accurate. I don't think a blanket "look for common" or "batch all together" approach is a good idea unless you have specific goals in mind, and understand the context of the data and what can be (should be) interpreted from the results.

But, as a start in evaluating your different datasets, you could try going a step further with them individually to see how they answer your larger questions. I'd start with some GO enrichment tools and evaluate. Then perhaps compare to alternate annotation sources. Some of these tools are available to use in Galaxy - check the Tool Shed and the Public Galaxy sites. And if your data is human in VCF, can use Annovar on the public Main site for a comprehensive annotation comparison.
http://wiki.galaxyproject.org/PublicGalaxyServers
http://usegalaxy.org/toolshed

ADD REPLY • link written 4.3 years ago by Jennifer Hillman Jackson ♦ 25k

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