User:Jose Fabricio Lopez/Notebook/GEDF/2012/10/02

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(Intergenic sequences in T.atroviride)
Line 16: Line 16:
====Things to do====
====Things to do====
*Analyze 20 matches.
*Analyze 20 matches.
-
*Correct mistakes in coordinates in 0bp file. run Blast to overview check.
+
*Correct mistakes in coordinates in 0bp file. Run Blast to overview check.
 +
*Prediction again by Augustus.
*Run analysis again with FilteringBLASTsFromAugustusPredictions.R in /Scripts & Data.
*Run analysis again with FilteringBLASTsFromAugustusPredictions.R in /Scripts & Data.
====Things done====
====Things done====
*Analyzed.
*Analyzed.
*Corrected.
*Corrected.
 +
*Prediction done.
*Re-analyzing.
*Re-analyzing.
===Loogbook===
===Loogbook===
*Just 20 hits. Seems there is something wrong. I see the coordinates in 0bp file and they are wrong!!! in file GettingSequences.R (I cant find the Script were I extract 0,480,1020,770), but this one works. And I create the file IntergenicFastaCorrected.fas (extracts just 0bp seqs).
*Just 20 hits. Seems there is something wrong. I see the coordinates in 0bp file and they are wrong!!! in file GettingSequences.R (I cant find the Script were I extract 0,480,1020,770), but this one works. And I create the file IntergenicFastaCorrected.fas (extracts just 0bp seqs).
 +
*Corrected.
 +
====Prediction====
 +
**'''Submitting JGI'''
 +
----------------------------------------
 +
Wed Oct 03 00:31:47 CEST 2012 - Message:
 +
----------------------------------------
 +
 +
Details of your job:
 +
 +
 +
Prediction job ID: predqHPrnxqC
 +
 +
Parameter archive: parameters.tar.gz
 +
 +
Genome file: IntergenicFastaCorrected.fas
 +
 +
User set UTR prediction: false
 +
 +
Report genes on: both strands
 +
 +
Alternative transcripts: none
 +
 +
Allowed gene structure: predict any number of (possibly partial) genes
 +
 +
Ignore conflictes with other strand: false
 +
 +
**'''Resutls JGI'''
 +
----------------------------------------
 +
Wed Oct 03 00:31:47 CEST 2012 - Message:
 +
----------------------------------------
 +
 +
Details of your job:
 +
 +
 +
Prediction job ID: predqHPrnxqC
 +
 +
Parameter archive: parameters.tar.gz
 +
 +
Genome file: IntergenicFastaCorrected.fas
 +
 +
User set UTR prediction: false
 +
 +
Report genes on: both strands
 +
 +
Alternative transcripts: none
 +
 +
Allowed gene structure: predict any number of (possibly partial) genes
 +
 +
Ignore conflictes with other strand: false
 +
 +
Your AUGUSTUS prediction job predqH**** finished.
 +
 +
 +
'''Submitting 454'''
 +
 +
----------------------------------------
 +
Wed Oct 03 00:42:29 CEST 2012 - Message:
 +
----------------------------------------
 +
 +
Details of your job:
 +
 +
 +
Prediction job ID: prediLs9Y6C3
 +
 +
Parameter archive: parameters.tar.gz
 +
 +
Genome file: IntergenicFastaCorrected.fas
 +
 +
User set UTR prediction: false
 +
 +
Report genes on: both strands
 +
 +
Alternative transcripts: none
 +
 +
Allowed gene structure: predict any number of (possibly partial) genes
 +
 +
Ignore conflictes with other strand: false
 +
 +
'''Results 454'''
 +
----------------------------------------
 +
Wed Oct 03 00:42:29 CEST 2012 - Message:
 +
----------------------------------------
 +
 +
Details of your job:
 +
 +
 +
Prediction job ID: prediLs9Y6C3
 +
 +
Parameter archive: parameters.tar.gz
 +
 +
Genome file: IntergenicFastaCorrected.fas
 +
 +
User set UTR prediction: false
 +
 +
Report genes on: both strands
 +
 +
Alternative transcripts: none
 +
 +
Allowed gene structure: predict any number of (possibly partial) genes
 +
 +
Ignore conflictes with other strand: false
 +
 +
Your AUGUSTUS prediction job prediLs9**** finished.
 +
*Re-analysing.
*Re-analysing.
 +
==Extras==
==Extras==
<!-- ##### DO NOT edit below this line unless you know what you are doing. ##### -->
<!-- ##### DO NOT edit below this line unless you know what you are doing. ##### -->

Revision as of 18:38, 2 October 2012

Gene Expression and Development in Fungi Main project page
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Contents

Trichoderma & P. vulgaris interaction

Things to do

  • Capture VOCs

Things done

  • Abort capture.

Loogbook

  • Many beans are contaminated with fungi. :( sadly we need to wait for a new opportunity and new set to measuer VOCs.

Intergenic sequences in T.atroviride

Things to do

  • Analyze 20 matches.
  • Correct mistakes in coordinates in 0bp file. Run Blast to overview check.
  • Prediction again by Augustus.
  • Run analysis again with FilteringBLASTsFromAugustusPredictions.R in /Scripts & Data.

Things done

  • Analyzed.
  • Corrected.
  • Prediction done.
  • Re-analyzing.

Loogbook

  • Just 20 hits. Seems there is something wrong. I see the coordinates in 0bp file and they are wrong!!! in file GettingSequences.R (I cant find the Script were I extract 0,480,1020,770), but this one works. And I create the file IntergenicFastaCorrected.fas (extracts just 0bp seqs).
  • Corrected.

Prediction

    • Submitting JGI

Wed Oct 03 00:31:47 CEST 2012 - Message:


Details of your job:


Prediction job ID: predqHPrnxqC

Parameter archive: parameters.tar.gz

Genome file: IntergenicFastaCorrected.fas

User set UTR prediction: false

Report genes on: both strands

Alternative transcripts: none

Allowed gene structure: predict any number of (possibly partial) genes

Ignore conflictes with other strand: false

    • Resutls JGI

Wed Oct 03 00:31:47 CEST 2012 - Message:


Details of your job:


Prediction job ID: predqHPrnxqC

Parameter archive: parameters.tar.gz

Genome file: IntergenicFastaCorrected.fas

User set UTR prediction: false

Report genes on: both strands

Alternative transcripts: none

Allowed gene structure: predict any number of (possibly partial) genes

Ignore conflictes with other strand: false

Your AUGUSTUS prediction job predqH**** finished.


Submitting 454


Wed Oct 03 00:42:29 CEST 2012 - Message:


Details of your job:


Prediction job ID: prediLs9Y6C3

Parameter archive: parameters.tar.gz

Genome file: IntergenicFastaCorrected.fas

User set UTR prediction: false

Report genes on: both strands

Alternative transcripts: none

Allowed gene structure: predict any number of (possibly partial) genes

Ignore conflictes with other strand: false

Results 454


Wed Oct 03 00:42:29 CEST 2012 - Message:


Details of your job:


Prediction job ID: prediLs9Y6C3

Parameter archive: parameters.tar.gz

Genome file: IntergenicFastaCorrected.fas

User set UTR prediction: false

Report genes on: both strands

Alternative transcripts: none

Allowed gene structure: predict any number of (possibly partial) genes

Ignore conflictes with other strand: false

Your AUGUSTUS prediction job prediLs9**** finished.

  • Re-analysing.

Extras

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