Athurva Gore
Jump to navigation
Jump to search
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
- Remove bisulfite conversion function - DONE
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"
- 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.
- Dr. Li's data showed that the last base pair of the ligation arm was important.
File:08 22 2008 JinLi Ligation Arm Base Dist.png
- Average expression was calculated using the "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.
- Average expression was calculated using the "makeHist.pl" file.
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 |