Haynes Lab:Notebook/Synthetic Biology and Bioinformatics for Predictable Control of Therapeutic Genes/2012/03/10: Difference between revisions

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==Entry title==
==Galaxy Data==
* Since score throws out important data when you make it any higher than the score that correlates with the signal value I set my filter at a score of 100 and a signal of 6 (this way we aren't acquiring any promoter regions that may have too low of a signal value). After joining clean promoter data on Galaxy with the BJ Hotspots 1 file I received a return of 2,260 regions that contained the H3k27me3 signal. I checked OLIG1, OLIG2, CDKN2A, AND MYT1 and they all show up on the the list of joined data. Instead of naming with gene tags it names with something like NM_001033581. Unfortunately, after trying numerous tracks RefSeq was the only one that seemed reasonable, which is why I was not able to get the convenient gene tag names.  
* Since score throws out important data when you make it any higher than the score that correlates with the signal value I set my filter at a score of 100 and a signal of 6 (this way we aren't acquiring any promoter regions that may have too low of a signal value). After joining clean promoter data on Galaxy with the BJ Hotspots 1 file I received a return of 2,260 regions that contained the H3k27me3 signal. I checked OLIG1, OLIG2, CDKN2A, AND MYT1 and they all show up on the the list of joined data. Instead of naming with gene tags it names with something like NM_001033581. Unfortunately, after trying numerous tracks RefSeq was the only one that seemed reasonable, which is why I was not able to get the convenient gene tag names.  
*For an example of what the Gene Browser output looks like with the custom track I have provided a screenshot of CDKN2A below.
*For an example of what the Gene Browser output looks like with the custom track I have provided a screenshot of CDKN2A below.

Revision as of 18:22, 10 March 2012

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Galaxy Data

  • Since score throws out important data when you make it any higher than the score that correlates with the signal value I set my filter at a score of 100 and a signal of 6 (this way we aren't acquiring any promoter regions that may have too low of a signal value). After joining clean promoter data on Galaxy with the BJ Hotspots 1 file I received a return of 2,260 regions that contained the H3k27me3 signal. I checked OLIG1, OLIG2, CDKN2A, AND MYT1 and they all show up on the the list of joined data. Instead of naming with gene tags it names with something like NM_001033581. Unfortunately, after trying numerous tracks RefSeq was the only one that seemed reasonable, which is why I was not able to get the convenient gene tag names.
  • For an example of what the Gene Browser output looks like with the custom track I have provided a screenshot of CDKN2A below.


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