Athurva Gore: Difference between revisions
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* Received CpG island probe code from Dr. Zhang. | * Received CpG island probe code from Dr. Zhang. | ||
* Need to make modifications discussed in meeting: | * Need to make modifications discussed in meeting: | ||
*Necessary modifications: | * Necessary modifications: | ||
**Remove bisulfite conversion function - DONE | ** Remove bisulfite conversion function - DONE | ||
Create dummy function that simply does not do a replacement, but creates fwd and rev strands | [code]Create dummy function that simply does not do a replacement, but creates fwd and rev strands | ||
Commented code to find/replace | Commented code to find/replace | ||
Question: parts we are looking at; do they have N's in them? Probably shouldn't. | Question: parts we are looking at; do they have N's in them? Probably shouldn't.[/code] | ||
**Remove CG score penalty - DONE | ** Remove CG score penalty - DONE | ||
in function getProbeList | in function getProbeList | ||
remove section starting with "my $CG_penalty" | remove section starting with "my $CG_penalty" | ||
set CG_penalty as always zero for quick fix, remove CG finding code later | 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) | ** 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 | Looks like function oligoFreq does this; currently just uses log of each side | ||
Modify probe score calculation to favor segment B being more unique | Modify probe score calculation to favor segment B being more unique | ||
See function getProbeList | See function getProbeList | ||
**Modify score calculation so that Tm of segment A should be high and Tm of segment B should be low | ** 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 | 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 | Simply modify to adjust so that A has high Tm, B has low Tm | ||
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Specific thresholds? | Specific thresholds? | ||
**Exon database | ** Exon database | ||
Ask about our current UCSC data; it comes in format on PGP server, or is this modified? | Ask about our current UCSC data; it comes in format on PGP server, or is this modified? | ||
Found Exon-Intron Database; uses GenBank | Found Exon-Intron Database; uses GenBank | ||
Show Dr. Zhang the readme | Show Dr. Zhang the readme |
Revision as of 17:06, 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
[code]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.[/code]
- 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