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>
** '''Remove CG score penalty - DONE'''
<calendar>
*** in function getProbeList
name=Athurva_Gore
*** remove section starting with "my $CG_penalty"
format=%name/LabNotes/%year-%month-%day
*** set CG_penalty as always zero for quick fix, remove CG finding code later
date=2011/01/06
** '''Add function to check sequence uniqueness in human genome (build hash table ahead of time, check Dr. Zhang's functions)'''
view=oneyear
*** Looks like function oligoFreq does this; currently just uses log of each side
</calendar>
*** Modify probe score calculation to favor segment B being more unique
<calendar>
*** See function getProbeList
name=Athurva_Gore
** '''Modify score calculation so that Tm of segment A should be high and Tm of segment B should be low'''
format=%name/LabNotes/%year-%month-%day
*** At the moment, Tm score is used in p_score calculation
date=2010/01/04
*** Simply modify to adjust so that A has high Tm, B has low Tm
view=oneyear
*** See function getProbeList
</calendar>
*** Specific thresholds?
<calendar>
** '''Exon database'''
name=Athurva_Gore
*** Ask about our current UCSC data; it comes in format on PGP server, or is this modified?
format=%name/LabNotes/%year-%month-%day
*** Found Exon-Intron Database; uses GenBank
date=2009/04/07
*** Show Dr. Zhang the readme
view=oneyear
</calendar>


==August 11th - August 17th==
=ROTATION STUFF BELOW=
* Will copy from notebook
=DNA Folding Energies=
==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.
**Earlier, Dr. Zhang's analysis on CES22K set used the following factors:
***ProbeDist: distribution of oligo abundance determined by Solexa sequencing. - '''Don't have this for the Cosmic set'''
***H1_Tm, H2_Tm: H1 (ligation arm), H2 (extension arm), 12bp sub-sequences of H1 and H2. - '''Normalized for the Cosmic set; very close to 62 C in all cases'''
***H1R_dist, H2L_dist: K-mer distribution of H1&H2 12bp sub-sequences in the human genome. - '''Have this'''
***Core_25bp_genomic_homology: weighted score of the 25bp homologous sequences in the human genome, mapped by SOAP with <=3bp mismatches. - '''Not sure what this is...ask Dr. Zhang'''


==August 28th==
=Lab Rotation=
*TO DO TODAY:
*Will add daily entries once schedule settles down a bit.
**Take log of various factors in R, see if this affects ''lm'' results.
*[[Athurva_Gore:LabNotes/LabRotation|Lab Rotation Notes]]
**See if any other combinations of factors produce better fits in R.
**Implement algorithm to select probes in Perl.
*'''R Analysis of Cosmic Data Set'''
**Tried taking the log of all factors aside from Tm, checked fit.
**Fit is still not very good
***Very low R^2 value
***Checked by plotting in Octave; fit does not match up to data well at all.
**Perhaps a different, non-linear, non-logarithmic model is needed?
**This would makes sense, as several of the data pieces seem to resemble a bell-curve shape...
***Intuitively, this also makes sense; if a factor is too low or too high, performance is decreased.

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]