User:Jose Fabricio Lopez/Notebook/GEDF/2012/10/02 - Revision history

Jose Fabricio Lopez: /* Things to do */

Jose Fabricio Lopez — Wed, 10 Oct 2012 17:25:16 GMT

Things to do

←Older revision		Revision as of 17:25, 10 October 2012
Line 9:		Line 9:
	====Things to do====		====Things to do====
	*Capture VOCs		*Capture VOCs
-	*Germinate new set of beans ~~(3)~~	+	*Germinate new set of beans 3rd
		+
	====Things done====		====Things done====
	*Abort capture.		*Abort capture.

Jose Fabricio Lopez: /* Trichoderma & P. vulgaris interaction */

Jose Fabricio Lopez — Wed, 03 Oct 2012 20:04:51 GMT

Trichoderma & P. vulgaris interaction

←Older revision		Revision as of 20:04, 3 October 2012
Line 9:		Line 9:
	====Things to do====		====Things to do====
	*Capture VOCs		*Capture VOCs
		+	*Germinate new set of beans (3)
	====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====

Jose Fabricio Lopez: /* Intergenic sequences in T.atroviride */

Jose Fabricio Lopez — Tue, 02 Oct 2012 22:38:25 GMT

Intergenic sequences in T.atroviride

←Older revision		Revision as of 22:38, 2 October 2012
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. ##### -->

Jose Fabricio Lopez at 22:13, 2 October 2012

Jose Fabricio Lopez — Tue, 02 Oct 2012 22:13:27 GMT

←Older revision		Revision as of 22:13, 2 October 2012
Line 8:		Line 8:
	==Trichoderma & P. vulgaris interaction==		==Trichoderma & P. vulgaris interaction==
	====Things to do====		====Things to do====
-		+	*Capture VOCs
	====Things done====		====Things done====
-		+	*Abort capture.
	===Loogbook===		===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==		==Intergenic sequences in T.atroviride==
	====Things to do====		====Things to do====
-		+	*Analyze 20 matches.
		+	*Correct mistakes in coordinates in 0bp file. run Blast to overview check.
		+	*Run analysis again with FilteringBLASTsFromAugustusPredictions.R in /Scripts & Data.
	====Things done====		====Things done====
-		+	*Analyzed.
		+	*Corrected.
		+	*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).
		+	*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. ##### -->

Jose Fabricio Lopez: Autocreate 2012/10/02 Entry for User:Jose_Fabricio_Lopez/Notebook/GEDF

Jose Fabricio Lopez — Tue, 02 Oct 2012 21:57:13 GMT

Autocreate 2012/10/02 Entry for User:Jose_Fabricio_Lopez/Notebook/GEDF

New page

{|{{table}} width="800"
|-
|style="background-color: #556B2F"|[[Image:Fungi.jpg|150px]]<span style="font-size:22px;"> Gene Expression and Development in Fungi</span>
|style="background-color: #228B22" align="center"|<html><img src="http://openwetware.org/images/9/94/Report.png" border="0" /></html> [[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>[[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]]<html>      </html>}}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]]<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>}}
|-
| colspan="2"|

==Trichoderma & P. vulgaris interaction==
====Things to do====

====Things done====

===Loogbook===

==Intergenic sequences in T.atroviride==
====Things to do====

====Things done====

===Loogbook===

==Extras==