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. | *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> </html>Next entry<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html> |
Trichoderma & P. vulgaris interactionThings to do
Things done
Loogbook
Intergenic sequences in T.atrovirideThings to do
Things done
Loogbook
Prediction
Wed Oct 03 00:31:47 CEST 2012 - Message: Details of your job:
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
Wed Oct 03 00:31:47 CEST 2012 - Message: Details of your job:
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.
Wed Oct 03 00:42:29 CEST 2012 - Message: Details of your job:
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:
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.
Extras |