User:Jose Fabricio Lopez/Notebook/GEDF/2012/10/02: Difference between revisions

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====Things to do====
====Things to do====
*Capture VOCs
*Capture VOCs
*Germinate new set of beans 3rd
====Things done====
====Things done====
*Abort capture.
*Abort capture.
*Germinating.
===Loogbook===
===Loogbook===
*Many beans are contaminated with fungi. :( sadly we need to wait for a new opportunity and new set to measuer VOCs.
*Many beans are contaminated with fungi. :( sadly we need to wait for a new opportunity and new set to measuer VOCs.
*This is a 3rd set of beans. This work was mady by Emmy.
==Intergenic sequences in T.atroviride==
==Intergenic sequences in T.atroviride==
====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. ##### -->

Latest revision as of 10:25, 10 October 2012

Gene Expression and Development in Fungi <html><img src="http://openwetware.org/images/9/94/Report.png" border="0" /></html> Main project page
<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>Previous entry<html>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</html>Next entry<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>

Trichoderma & P. vulgaris interaction

Things to do

  • Capture VOCs
  • Germinate new set of beans 3rd

Things done

  • Abort capture.
  • Germinating.

Loogbook

  • Many beans are contaminated with fungi. :( sadly we need to wait for a new opportunity and new set to measuer VOCs.
  • This is a 3rd set of beans. This work was mady by Emmy.

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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