User:Jose Fabricio Lopez/Notebook/GEDF/2012/08/27: Difference between revisions

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==Trichoderma & A. thaliana interaction==
==Trichoderma & A. thaliana interaction==
====Things to do====
====Things to do====
 
*Check plants
*Move to soil plants
====Things done====
====Things done====
*Plants were checked
*Unfortunatly our seeds were polluted. And Emmy and me are no having succesful number of growth seeds.


===Loogbook===
===Loogbook===
 
*Nothing to say
==Intergenic sequences in T.atroviride==
==Intergenic sequences in T.atroviride==
====Things to do====
====Things to do====
 
*Extract whole intergenic sequences of Trichoderma atroviride.
====Things done====
====Things done====
 
*Half on the way.
===Loogbook===
===Loogbook===
 
*Unfortunately genomme is not well annotated, I mean, the file .gff in [http://genome.jgi-psf.org/Triat2/Triat2.download.ftp.html JGI], have somo problems. Some IDs are part of the all models. This gives me problems.
*To avoid problems I used IRanges, in order to "reduce()" the coords of Conding Zones and leaving Intergenic By Strand apart.
*GettingWholeIntergenicSequences.R file.
==Extras==
==Extras==
 
*There are no extras
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Latest revision as of 17:47, 27 August 2012

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Trichoderma & A. thaliana interaction

Things to do

  • Check plants
  • Move to soil plants

Things done

  • Plants were checked
  • Unfortunatly our seeds were polluted. And Emmy and me are no having succesful number of growth seeds.

Loogbook

  • Nothing to say

Intergenic sequences in T.atroviride

Things to do

  • Extract whole intergenic sequences of Trichoderma atroviride.

Things done

  • Half on the way.

Loogbook

  • Unfortunately genomme is not well annotated, I mean, the file .gff in JGI, have somo problems. Some IDs are part of the all models. This gives me problems.
  • To avoid problems I used IRanges, in order to "reduce()" the coords of Conding Zones and leaving Intergenic By Strand apart.
  • GettingWholeIntergenicSequences.R file.

Extras

  • There are no extras
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