Athurva Gore: Difference between revisions
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=Lab Rotation= | =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 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 |
Revision as of 17:05, 11 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 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