User:Jose Fabricio Lopez/Notebook/GEDF/2012/09/04: Difference between revisions

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==Trichoderma & P. vulgaris interaction==
==Trichoderma & P. vulgaris interaction==
====Things to do====
====Things to do====
 
*Pass seeds to soil
====Things done====
====Things done====
 
*Seeds passed.
===Loogbook===
===Loogbook===
 
*We are have not a designated place to our work, so, we are using greenhouse max ~28°C.
*20 seeds in total.
**10 inoculated
**10 free of Trichoderma.
*We are going to measure biomass, true leaves, root size, some pathologies and number of beans per plant.
==Intergenic sequences in T.atroviride==
==Intergenic sequences in T.atroviride==
====Things to do====
====Things to do====
*Wait for a training set of T.atroviride.
*Submit the test to prediction.
*Results of prediction, compare predicted genes with FrozenGeneCatalog of T.atro.
====Things done====
*Results of training.
*Submitted. Finished.
*Still runing BLAST
===Loogbook===
*This is the result of the training.


====Things done====
<code>
----------------------------------------
Mon Sep 03 22:36:29 CEST 2012 - Message:
----------------------------------------
 
Details of your job:
 
Training job ID: trainc2HM4EWp
Species name: Trichoderma_atroviride
Genome file: Trichoderma_atroviride_v2.fasta
cDNA file: 454Isotigs.fna
Training gene structure file: Tatroviridev2_FrozenGeneCatalog_20100319.gff
 
----------------------------------------------
Tue Sep 04 05:27:27 CEST 2012 - Error Message:
----------------------------------------------
 
An error occured while running the AUGUSTUS training job trainc2HM4EWp.


===Loogbook===
</code>


I think this could be owed to lack of UTR predictions. As shows
*
==Extras==
==Extras==


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Revision as of 17:26, 4 September 2012

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Trichoderma & P. vulgaris interaction

Things to do

  • Pass seeds to soil

Things done

  • Seeds passed.

Loogbook

  • We are have not a designated place to our work, so, we are using greenhouse max ~28°C.
  • 20 seeds in total.
    • 10 inoculated
    • 10 free of Trichoderma.
  • We are going to measure biomass, true leaves, root size, some pathologies and number of beans per plant.

Intergenic sequences in T.atroviride

Things to do

  • Wait for a training set of T.atroviride.
  • Submit the test to prediction.
  • Results of prediction, compare predicted genes with FrozenGeneCatalog of T.atro.

Things done

  • Results of training.
  • Submitted. Finished.
  • Still runing BLAST

Loogbook

  • This is the result of the training.

Mon Sep 03 22:36:29 CEST 2012 - Message:

Details of your job:

Training job ID: trainc2HM4EWp Species name: Trichoderma_atroviride Genome file: Trichoderma_atroviride_v2.fasta cDNA file: 454Isotigs.fna Training gene structure file: Tatroviridev2_FrozenGeneCatalog_20100319.gff

Tue Sep 04 05:27:27 CEST 2012 - Error Message:

An error occured while running the AUGUSTUS training job trainc2HM4EWp.

I think this could be owed to lack of UTR predictions. As shows

Extras
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