User:Jose Fabricio Lopez/Notebook/GEDF/2012/09/12: Difference between revisions
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====Things to do==== | ====Things to do==== | ||
*Check BLAST btwn t.at.both vs ncrna. | *Check BLAST btwn t.at.both vs ncrna. | ||
*Analyze results from Augus pred vs TrichodermaFrozen. | *Analyze results from [[User:Jose Fabricio Lopez/Notebook/GEDF/2012/09/04| Augus pred]] vs TrichodermaFrozen. | ||
*Run BLAST of Augus vsTrichodermaFrozen with less e-value. | |||
*Training Agusutus with JGI ESTs. | |||
*Run prediction Augustus with 0bp away gene set. | |||
*Run prediction Augustus with both set. | |||
====Things done==== | ====Things done==== | ||
*Checked BLAST btwn t.at.both vs ncrna. | *Checked BLAST btwn t.at.both vs ncrna. | ||
*Analyzing | *Analyzing | ||
*Running | |||
*Job submitted and running with JGI EST. | |||
*0bp away gene set. Job submitted | |||
*BOTH gene set. Job submitted | |||
===Loogbook=== | ===Loogbook=== | ||
=====BLAST btwn t.at.both vs ncrna===== | |||
*No hits found in BLAST btwn t.at.both vs ncrna. | *No hits found in BLAST btwn t.at.both vs ncrna. | ||
<code> | <code> | ||
-evalue 1e-3 -num_alignments 10 -query RealIntergenicBOTH.fas -out BLASTnTotalIntergenicRegionsVsncrnaDB.txt -word_size 4 -outfmt 6 | -evalue 1e-3 -num_alignments 10 -query RealIntergenicBOTH.fas -out BLASTnTotalIntergenicRegionsVsncrnaDB.txt -word_size 4 -outfmt 6 | ||
</code> | |||
=====Augus pred vs TrichodermaFrozen===== | |||
* 13538 hits found. | |||
**9326 100% of identity. | |||
**5778 of e-value | |||
**9694 uniq names with hit this means predicted almost. | |||
* Sesibility= .78 | |||
<code> | |||
TrichodermaAtrovirideV2.aa -evalue 1e-5 -num_alignments 1 -query augustusPredictionTestResults.aa -out BLASTTestAugustusVsTrichodremaFrozenGene.txt -word_size 7 -outfmt 6 | |||
</code> | |||
=====BLAST e-value 1e-3===== | |||
In order to get more hits I run blast again. e-value 1e-3. It is made just in case. Between Agustus predicted and T.at.v2.aa | |||
=====JGI ESTs trainning===== | |||
<code> | |||
Training job ID: train7t4v7v8r | |||
Species name: Trichoderma_atroviride.JGI | |||
Genome file: Trichoderma_atroviride_v2.fasta | |||
Training gene structure file: Tatroviridev2_FrozenGeneCatalog_20100319.gff | |||
</code> | |||
=====Prediction of 0bp away===== | |||
Made with parameters given by [http://openwetware.org/wiki/User:Jose_Fabricio_Lopez/Notebook/GEDF/2012/09/04 training]. With personal isotigs.fna | |||
'''Submitting''' | |||
<code> | |||
Prediction job ID: predds5qadkd | |||
Parameter archive: parameters.tar.gz | |||
Genome file: ****Fasta.fna | |||
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 | |||
</code> | |||
'''Results''' | |||
<code> | |||
---------------------------------------- | |||
Wed Sep 12 22:28:30 CEST 2012 - Message: | |||
---------------------------------------- | |||
Details of your job: | |||
Prediction job ID: predds5qadkd | |||
Parameter archive: parameters.tar.gz | |||
Genome file: IntergenicFasta.fna | |||
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 | |||
</code> | </code> | ||
=====Augustus BOTH set===== | |||
'''Submitting''' | |||
<code> | <code> | ||
---------------------------------------- | |||
Sep 13 00:01:40 CEST 2012 - Message: | |||
---------------------------------------- | |||
Details of your job: | |||
Prediction job ID: predKmQCPAiD | |||
Parameter archive: parameters.tar.gz | |||
Genome file: RealIntergenicBOTH.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 | |||
</code> | |||
'''Results''' | |||
<code> | |||
---------------------------------------- | |||
Thu Sep 13 00:01:40 CEST 2012 - Message: | |||
---------------------------------------- | |||
Details of your job: | |||
Prediction job ID: predKmQCPAiD | |||
Parameter archive: parameters.tar.gz | |||
Genome file: RealIntergenicBOTH.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 predKmQCPAiD finished. | |||
</code> | </code> | ||
Latest revision as of 10:21, 13 September 2012
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Trichoderma & P. vulgaris interactionThings to doThings doneLoogbookIntergenic sequences in T.atrovirideThings to do
Things done
LoogbookBLAST btwn t.at.both vs ncrna
Augus pred vs TrichodermaFrozen
BLAST e-value 1e-3In order to get more hits I run blast again. e-value 1e-3. It is made just in case. Between Agustus predicted and T.at.v2.aa JGI ESTs trainning
Prediction of 0bp awayMade with parameters given by training. With personal isotigs.fna Submitting
Results
Augustus BOTH setSubmitting
Results
Extras |