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Question: Is there a tool for displaying statistics result of a gene ?
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gravatar for jchen015
3.6 years ago by
jchen015 • 80
Singapore
jchen015 • 80 wrote:

Dear All

Is there an existing tool which could do a search on existing genes and print out the short reads in the genes?

For example (reference the link here: https://www.dropbox.com/s/04f6uemsljlcott/20150414_004523.jpg?dl=0 )

 

Regards,

Julius
counting_reads • 644 views
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modified 3.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.6 years ago by jchen015 • 80
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gravatar for Jennifer Hillman Jackson
3.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If you have transcripts with associated gene names mapped to the same reference genome as the short reads, then this is fairly simple to do. A similar example comparison is done in a few of our tutorials. The basic path is to 1.) compare the two sets of coordinates and then 2.) summarize by one of them. If you need to map transcript name to gene name, or merge that with the coordinates, that type of operation is covered too. 

Here are the examples to learn from:

  1. http://usegalaxy.org/u/galaxyproject/p/using-galaxy-2012 Protocol's 1 & 2
  2. http://usegalaxy.org/u/aun1/p/galaxy101

Hope this helps! Jen, Galaxy team
ADD COMMENT • link written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k
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