Athurva Gore: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Ajgore
>Ajgore
No edit summary
 
(83 intermediate revisions by the same user not shown)
Line 1: Line 1:
* [[Athurva_Gore:LabNotes/LabMeetings|Lab Presentations]]
* [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)]]
=Overall Notes=
* [[Athurva_Gore:IupacAmbiguity|IUPAC Ambiguity Codes for SNPs]]
<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=
=DNA Folding Energies=
=Lab Rotation=
=Lab Rotation=
*Will add daily entries once schedule settles down a bit.
*Will add daily entries once schedule settles down a bit.
 
*[[Athurva_Gore:LabNotes/LabRotation|Lab Rotation Notes]]
==August 4th - August 10th==
* Received CpG island probe code from Dr. Zhang.
* Need to make modifications discussed in meeting:
* Necessary modifications:
** '''Remove bisulfite conversion function - DONE'''
*** Create dummy function that simply does not do a replacement, but creates fwd and rev strands
*** Commented code to find/replace
*** Question:  parts we are looking at; do they have N's in them?  Probably shouldn't.
** '''Remove CG score penalty - DONE'''
*** in function getProbeList
*** 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 Dr. Zhang's functions)'''
*** Looks like function oligoFreq does this; currently just uses log of each side
*** Modify probe score calculation to favor segment B being more unique
*** 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
 
==August 11th - August 17th==
* Will copy from notebook
==August 18th - August 24th==
* Will copy from Notebook
==August 27th==
* Have code to read and analyze Cosmic set data; file is [[Media:ReadCosmic_20080827.txt‎|"readCosmic.pl"]]
* '''Comparison of Cosmic set data to Dr. Li's data (Harvard Collaborator)'''
** Dr. Li's data showed that the last base pair of the ligation arm was important.
*** Dr. Li checked average expression for each base.
*** G was preferred for ligation, followed by A, C, and T.
[[Image:08_22_2008_JinLi_Ligation_Arm_Base_Dist.png]]
** Average expression was calculated using the [[Media:MakeHist_20080827.txt|"makeHist.pl"]] file.
*** This file averages the abundance of the probes that used each base.
** The results were slightly different.
*** For the COSMIC set, it was found that for the proximal ligation arm, G was preferred, followed by C, A, and T.
*** This makes intuitive sense, as the bond between G and C is stronger than the bond between A and T.
*** The results were also much less pronounced than Dr. Li's results; the difference in base performance is much smaller.
{|border="1" cellpadding="5" cellspacing="0"
| align="center" colspan="21" | '''Cosmic Set Results'''
|-
|'''Base:'''||A||T||G||C
|-
|'''Proximal Extension Arm:'''||98.2276826484018||105.4814504701790||97.8751164168995||105.1120477176380
|-
|'''Distal Extension Arm:'''||104.9745183977170||107.4126226040130||106.5526921141540||88.8525735059634
|-
|'''Proximal Ligation Arm:'''||95.1374247734938||83.7531848897751||135.360909000299||107.876484056988
|-
|'''Distal Ligation Arm:'''||103.1547820103830||113.0664396095970||96.5690024678530||96.7110820814283
|}
[[Image:Proximal_Ligation_Base.png]]
** Analyze these results later; perhaps add in a preference on the Proximal Ligation Arm to favor G or C over A or T in the score.
*'''Implementation of new probe set algorithm.'''
** Algorithm is summarized above.
** Implement in Perl using hash table in getCpGIslands.pl file.
*'''Use R to analyze Cosmic Data Set'''
** Downloaded and installed GNU R and R-commander (GUI)
** Can load CSV and tab-separated files.
** ''lm'' command can do a linear model fit to the data.
*** May need to take the log of several pieces of data however in order to improve fit (if data is exponentially correlated).
** Initial ''lm'' results for Cosmic set show a very poor correlation...probably need to take log of several pieces of data set.

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]