Athurva Gore: Difference between revisions

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=Lab Rotation=
* [[Athurva_Gore:LabNotes/LabMeetings|Lab Presentations]]
*Will add daily entries once schedule settles down a bit.
* [http://genome-tech.ucsd.edu/LabNotes/probedesign Probe Designer]
* [[Athurva_Gore:LabNotes/PrimerDes|PCR Primer Design Instructions]]
* [[Athurva_Gore:LabNotes/ExomePipeline|Human Genome Resequencing Pipeline]]
=Current Tasks=
* [[Athurva_Gore:LabNotes/RnaEditing|RNA Editing]]
* [[Athurva_Gore:LabNotes/ExomeReseq|Exome Resequencing (PGP)]]


==August 4th - August 10th==
=Overall Notes=
* Received CpG island probe code from Dr. Zhang.
* [[Athurva_Gore:IupacAmbiguity|IUPAC Ambiguity Codes for SNPs]]
* Need to make modifications discussed in meeting:
<calendar>
*Necessary modifications:
name=Athurva_Gore
**Remove bisulfite conversion function - DONE
format=%name:LabNotes/%year-%month-%day
Create dummy function that simply does not do a replacement, but creates fwd and rev strands
date=2012/01/03
Commented code to find/replace
view=oneyear
Question:  parts we are looking at; do they have N's in them?  Probably shouldn't.
</calendar>
<calendar>
name=Athurva_Gore
format=%name/LabNotes/%year-%month-%day
date=2011/01/06
view=oneyear
</calendar>
<calendar>
name=Athurva_Gore
format=%name/LabNotes/%year-%month-%day
date=2010/01/04
view=oneyear
</calendar>
<calendar>
name=Athurva_Gore
format=%name/LabNotes/%year-%month-%day
date=2009/04/07
view=oneyear
</calendar>


**Remove CG score penalty - DONE
=ROTATION STUFF BELOW=
in function getProbeList
=DNA Folding Energies=
remove section starting with "my $CG_penalty"
set CG_penalty as always zero for quick fix, remove CG finding code later


**Add function to check sequence uniqueness in human genome (build hash table ahead of time, check Zhang's functions)
=Lab Rotation=
Looks like function oligoFreq does this; currently just uses log of each side
*Will add daily entries once schedule settles down a bit.
Modify probe score calculation to favor segment B being more unique
*[[Athurva_Gore:LabNotes/LabRotation|Lab Rotation Notes]]
See function getProbeList
 
**Modify score calculation so that Tm of segment A should be high and Tm of segment B should be low
At the moment, Tm score is used in p_score calculation
Simply modify to adjust so that A has high Tm, B has low Tm
See function getProbeList
Specific thresholds?
 
**Exon database
Ask about our current UCSC data; it comes in format on PGP server, or is this modified?
Found Exon-Intron Database; uses GenBank
Show Dr. Zhang the readme

Latest revision as of 19:30, 16 February 2012

Current Tasks[edit]

Overall Notes[edit]

<calendar> name=Athurva_Gore format=%name:LabNotes/%year-%month-%day date=2012/01/03 view=oneyear </calendar> <calendar> name=Athurva_Gore format=%name/LabNotes/%year-%month-%day date=2011/01/06 view=oneyear </calendar> <calendar> name=Athurva_Gore format=%name/LabNotes/%year-%month-%day date=2010/01/04 view=oneyear </calendar> <calendar> name=Athurva_Gore format=%name/LabNotes/%year-%month-%day date=2009/04/07 view=oneyear </calendar>

ROTATION STUFF BELOW[edit]

DNA Folding Energies[edit]

Lab Rotation[edit]