Athurva Gore: Difference between revisions

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** Dr. Li's data showed that the last base pair of the ligation arm was important.
** Dr. Li's data showed that the last base pair of the ligation arm was important.
*** Dr. Li checked average expression for each base.
*** Dr. Li checked average expression for each base.
*** G was preferred for ligation, followed by A, C, and T. ('''UPLOAD DR. LI's DATA''')
*** G was preferred for ligation, followed by A, C, and T.
[[Image:08_22_2008_JinLi_Ligation_Arm_Base_Dist.png]]
[[Image:08_22_2008_JinLi_Ligation_Arm_Base_Dist.png]]
** Average expression was calculated using the "makeHist.pl" file ('''NEED TO UPLOAD''')
** Average expression was calculated using the "makeHist.pl" file ('''NEED TO UPLOAD''')

Revision as of 19:48, 27 August 2008

Lab Rotation

  • Will add daily entries once schedule settles down a bit.

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 "readCosmic.pl" (NEED TO UPLOAD)
  • 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.

File:08 22 2008 JinLi Ligation Arm Base Dist.png

    • Average expression was calculated using the "makeHist.pl" file (NEED TO UPLOAD)
      • 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 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.
Cosmic Set Results
Base: A T G C
Average Expression: 95.1374247734938 83.7531848897751 135.360909000299 107.876484056988