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Question: Non-Coding Rna
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gravatar for dongdong zhaoweiming
7.2 years ago by
dongdong zhaoweiming • 110
dongdong zhaoweiming • 110 wrote:
Hi, I want to evaluate wherther my assembly transcripts produced by trinity is protein-coding or notcoding. I found two methods which are  "txCdsPredict" program from the UCSC(John R Prensner,2011) and Codon Substitution Frequencies,CSF(Michael F. Lin,2008). I wonder if galaxy can do this? Thanks a lot!   weimin zhao
assembly • 919 views
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modified 7.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.2 years ago by dongdong zhaoweiming • 110
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gravatar for Jennifer Hillman Jackson
7.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello, The general analysis path would be: 1 - Map the transcripts to a reference genome to obtain location coordinates. One option is BLAST, which has a wrapper in the Tool Shed See http://galaxyproject.org/wiki/Tool%20Shed 2 - Import known protein-coding and non-protein coding tracks. See "Get Data" 3 - Use an intersection query to identify overlapping regions between the datasets to obtain annotation See "Operate on Genomic Intervals" The first mapping step would require a local or cloud instance, the other steps can be done within the public Galaxy or your own. Help: http://galaxyproject.org/wiki/Admin/Get%20Galaxy Best wishes for your project! Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
ADD COMMENT • link written 7.2 years ago by Jennifer Hillman Jackson ♦ 25k
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