Question: How to prepare param.yaml file of GLEAN for gene predictions from Augustus and GlimmerHMM?
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gravatar for jesvinjoy35
16 months ago by
jesvinjoy350 wrote:

Hi, I am trying to create a consensus get set using GLEAN. The input files I am using are gene predictions from Augustus, GlimmerHMM and GenScan. I have loaded the input files into MySql database. However, I want to know is there any syntax for the Augustus and GlimmerHmm gene predictions in the "param.yaml" file or How to prepare the "param.yaml" for gene predictions from Augustus, GlimmerHMM and GenScan?

glean assembly • 651 views
ADD COMMENTlink modified 16 months ago • written 16 months ago by jesvinjoy350
0
gravatar for jesvinjoy35
16 months ago by
jesvinjoy350 wrote:

After contacting the author of the tool, I came to know that this tool is no longer supported, The author himself told me not to use this tool. However, the answer to the question is given below.

param.yaml:

evidence:
  GeneModel:
    Augustus:
      types: "coding:AUGUSTUS"

    Genscan:
      types: "coding:Genscan"

    GlimmerHMM:
      types: "coding:GlimmerHMM"

params:
  start:
    freq: 0.5
  stop:
    freq: 0.5
  donor:
    freq:
      value: 0.5
      fixed: 0
  acceptor:
    freq: 0.5
ADD COMMENTlink written 16 months ago by jesvinjoy350
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