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Question: annotation and analysis indel of Bos tarus
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gravatar for 313315597
4.6 years ago by
313315597 • 0
Australia
313315597 • 0 wrote:

Dear,

   I have no experience about programming, and never do some research about bioinfomatics. so I want to find some answer about my issue.

    I have many NGS data--Indel about Cow, and I have tried my best to annotate them, so I got the different regions indels, but I even didnot know it is correct, and I do not find any efficient methods to do the next analysis either. would you give some better suggestion for my problem. I am looking forward to your apply. Thank you so much.
galaxy • 920 views
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modified 4.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.6 years ago by 313315597 • 0
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gravatar for Jennifer Hillman Jackson
4.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

On usegalaxy.org, tools to summarize/annotate .vcf files are under the tool group "NGS:Variant Analysis". You mapped versus one of the UCSC bosTau genomes? Give these two a try first:

  1. Variant Annotator - will filter and summarize your data into a dataset that is easier to review and manipulate (graph, etc)
  2. ANNOVAR - will annotate your data versus almost any annotation track that UCSC provides for this genome (you can extract the data with "Get Data -> UCSC Main). Click through to the ANNOVAR help to understand the input formats - this is clearly explained by the tool authors. (Other annotation sources are possible, but as with all tools, when providing inputs - the reference genome must be a match AND the identifiers in the datasets must be an exact match).

Then, after these, explore the others and decide which tools give you the most useful information for your own project. The Tool Shed has even more options for use in a cloud/local Galaxy. 

Thanks! Jen, Galaxy team
ADD COMMENT • link written 4.6 years ago by Jennifer Hillman Jackson ♦ 25k
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