Athurva Gore/LabNotes/2009-8-19: Difference between revisions
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* 18 bp SNP ProbeSet (cDNA version) | * 18 bp SNP ProbeSet (cDNA version) | ||
** http://genome-tech.ucsd.edu/LabNotes/upload/d/d8/PROBESET_18bp_SNP.txt | ** http://genome-tech.ucsd.edu/LabNotes/upload/d/d8/PROBESET_18bp_SNP.txt | ||
** Filtering was off for this set; an offset of -1000 was used if a probe failed a quality check | |||
** Parameters: | ** Parameters: | ||
our $exon_info_file='/Users/ajgore/Software/PPDesign/Jobs/Harvard_Lee/ZhangGenes_input_final.csv'; | |||
our $primerMaxLen=30; | |||
our $primerMinLen=18; | |||
our $H1OptLen=25; | |||
our $H2OptLen=25; | |||
our $targetOptLen=18; | |||
our $targetMinLen=18; | |||
our $targetMaxLen=18; | |||
our $arewebisulfite=0; | |||
our $softwareDir='/Users/ajgore/Software/PPDesign/07162009'; | |||
our $HsDir='/Users/kunzhang/HsGenome/hg18.snp129Mask/'; | |||
eval `cat $softwareDir/probe_parameters.pl` or die 'couldnt parse file'; | |||
eval `cat $softwareDir/load_inputs.pl` or die 'couldnt parse file'; | |||
eval `cat $softwareDir/get_sequence.pl` or die 'couldnt parse file'; | |||
eval `cat $softwareDir/get_probes_FixedTargets.pl` or die 'couldnt parse file'; | |||
eval `cat $softwareDir/neural_net.pl` or die 'couldnt parse file'; | |||
eval `cat $softwareDir/output_text.pl` or die 'couldnt parse file'; | |||
* Dr. Lee Probesets (18 bp SNP, cDNA) | * Dr. Lee Probesets (18 bp SNP, cDNA) | ||
** http://genome-tech.ucsd.edu/LabNotes/upload/8/82/PROBESET_LeeCancer_output_cDNA.txt | ** http://genome-tech.ucsd.edu/LabNotes/upload/8/82/PROBESET_LeeCancer_output_cDNA.txt | ||
** http://genome-tech.ucsd.edu/LabNotes/upload/9/9e/PROBESET_LeeXGenes_output_cDNA.txt | ** http://genome-tech.ucsd.edu/LabNotes/upload/9/9e/PROBESET_LeeXGenes_output_cDNA.txt | ||
** Filtering was off for this set; an offset of -1000 was used if a probe failed a quality check | |||
** Parameters: | ** Parameters: | ||
our $exon_info_file='/Users/ajgore/Software/PPDesign/Jobs/Harvard_Lee/CancerGenes_input_final.txt'; | |||
OR | |||
our $exon_info_file='/Users/ajgore/Software/PPDesign/Jobs/Harvard_Lee/XGenes/XchrGenes_input.txt'; | |||
our $primerMaxLen=30; | |||
our $primerMinLen=18; | |||
our $H1OptLen=25; | |||
our $H2OptLen=25; | |||
our $targetOptLen=18; | |||
our $targetMinLen=18; | |||
our $targetMaxLen=18; | |||
our $arewebisulfite=0; | |||
our $softwareDir='/Users/ajgore/Software/PPDesign/07162009'; | |||
our $HsDir='/Users/kunzhang/HsGenome/hg18.snp129Mask/'; | |||
eval `cat $softwareDir/probe_parameters.pl` or die 'couldnt parse file'; | |||
eval `cat $softwareDir/load_inputs.pl` or die 'couldnt parse file'; | |||
eval `cat $softwareDir/get_sequence.pl` or die 'couldnt parse file'; | |||
eval `cat $softwareDir/get_probes_FixedTargets.pl` or die 'couldnt parse file'; | |||
eval `cat $softwareDir/neural_net.pl` or die 'couldnt parse file'; | |||
eval `cat $softwareDir/output_text.pl` or die 'couldnt parse file'; | |||
* Baylor Probesets | * Baylor Probesets | ||
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** FLYDUP5279 is still running on genome-tech | ** FLYDUP5279 is still running on genome-tech | ||
** Parameters: | ** Parameters: | ||
our $exon_info_file='/Users/ajgore/Software/PPDesign/Jobs/Baylor/SETNAME/FILENAME'; | |||
our $primerMaxLen=30; | |||
our $primerMinLen=20; | |||
our $H1OptLen=25; | |||
our $H2OptLen=25; | |||
our $targetOptLen=170; | |||
our $targetMinLen=130; | |||
our $targetMaxLen=185; | |||
our $arewebisulfite=0; | |||
our $softwareDir='/Users/ajgore/Software/PPDesign/07162009'; | |||
our $HsDir='/Users/kunzhang/DmGenome/dm3/' OR '/Users/kunzhang/HsGenome/hg18.snpMask/'; | |||
eval `cat $softwareDir/probe_parameters.pl` or die 'couldnt parse file'; | |||
eval `cat $softwareDir/load_inputs.pl` or die 'couldnt parse file'; | |||
eval `cat $softwareDir/get_sequence.pl` or die 'couldnt parse file'; | |||
eval `cat $softwareDir/get_probes.pl` or die 'couldnt parse file'; | |||
eval `cat $softwareDir/neural_net.pl` or die 'couldnt parse file'; | |||
eval `cat $softwareDir/output_text.pl` or die 'couldnt parse file'; | |||
=Analyzing False Positives= | =Analyzing False Positives= |
Revision as of 17:42, 20 August 2009
Probeset Upload
- 18 bp SNP ProbeSet (cDNA version)
- http://genome-tech.ucsd.edu/LabNotes/upload/d/d8/PROBESET_18bp_SNP.txt
- Filtering was off for this set; an offset of -1000 was used if a probe failed a quality check
- Parameters:
our $exon_info_file='/Users/ajgore/Software/PPDesign/Jobs/Harvard_Lee/ZhangGenes_input_final.csv'; our $primerMaxLen=30; our $primerMinLen=18; our $H1OptLen=25; our $H2OptLen=25; our $targetOptLen=18; our $targetMinLen=18; our $targetMaxLen=18; our $arewebisulfite=0; our $softwareDir='/Users/ajgore/Software/PPDesign/07162009'; our $HsDir='/Users/kunzhang/HsGenome/hg18.snp129Mask/'; eval `cat $softwareDir/probe_parameters.pl` or die 'couldnt parse file'; eval `cat $softwareDir/load_inputs.pl` or die 'couldnt parse file'; eval `cat $softwareDir/get_sequence.pl` or die 'couldnt parse file'; eval `cat $softwareDir/get_probes_FixedTargets.pl` or die 'couldnt parse file'; eval `cat $softwareDir/neural_net.pl` or die 'couldnt parse file'; eval `cat $softwareDir/output_text.pl` or die 'couldnt parse file';
- Dr. Lee Probesets (18 bp SNP, cDNA)
- http://genome-tech.ucsd.edu/LabNotes/upload/8/82/PROBESET_LeeCancer_output_cDNA.txt
- http://genome-tech.ucsd.edu/LabNotes/upload/9/9e/PROBESET_LeeXGenes_output_cDNA.txt
- Filtering was off for this set; an offset of -1000 was used if a probe failed a quality check
- Parameters:
our $exon_info_file='/Users/ajgore/Software/PPDesign/Jobs/Harvard_Lee/CancerGenes_input_final.txt'; OR our $exon_info_file='/Users/ajgore/Software/PPDesign/Jobs/Harvard_Lee/XGenes/XchrGenes_input.txt'; our $primerMaxLen=30; our $primerMinLen=18; our $H1OptLen=25; our $H2OptLen=25; our $targetOptLen=18; our $targetMinLen=18; our $targetMaxLen=18; our $arewebisulfite=0; our $softwareDir='/Users/ajgore/Software/PPDesign/07162009'; our $HsDir='/Users/kunzhang/HsGenome/hg18.snp129Mask/'; eval `cat $softwareDir/probe_parameters.pl` or die 'couldnt parse file'; eval `cat $softwareDir/load_inputs.pl` or die 'couldnt parse file'; eval `cat $softwareDir/get_sequence.pl` or die 'couldnt parse file'; eval `cat $softwareDir/get_probes_FixedTargets.pl` or die 'couldnt parse file'; eval `cat $softwareDir/neural_net.pl` or die 'couldnt parse file'; eval `cat $softwareDir/output_text.pl` or die 'couldnt parse file';
- Baylor Probesets
- http://genome-tech.ucsd.edu/LabNotes/upload/5/50/PROBESET_Baylor_RPLCACRD_output_final.txt
- http://genome-tech.ucsd.edu/LabNotes/index.php/Image:PROBESET_Baylor_KKESH72_output_final.txt
- http://genome-tech.ucsd.edu/LabNotes/upload/1/1b/PROBESET_Baylor_FlyDup936_output_final.txt
- http://genome-tech.ucsd.edu/LabNotes/upload/9/9d/PROBESET_Baylor_FlyDup901_output_final.txt
- FLYDUP5279 is still running on genome-tech
- Parameters:
our $exon_info_file='/Users/ajgore/Software/PPDesign/Jobs/Baylor/SETNAME/FILENAME'; our $primerMaxLen=30; our $primerMinLen=20; our $H1OptLen=25; our $H2OptLen=25; our $targetOptLen=170; our $targetMinLen=130; our $targetMaxLen=185; our $arewebisulfite=0; our $softwareDir='/Users/ajgore/Software/PPDesign/07162009'; our $HsDir='/Users/kunzhang/DmGenome/dm3/' OR '/Users/kunzhang/HsGenome/hg18.snpMask/'; eval `cat $softwareDir/probe_parameters.pl` or die 'couldnt parse file'; eval `cat $softwareDir/load_inputs.pl` or die 'couldnt parse file'; eval `cat $softwareDir/get_sequence.pl` or die 'couldnt parse file'; eval `cat $softwareDir/get_probes.pl` or die 'couldnt parse file'; eval `cat $softwareDir/neural_net.pl` or die 'couldnt parse file'; eval `cat $softwareDir/output_text.pl` or die 'couldnt parse file';
Analyzing False Positives
- G-A bias? Check, Rob noticed it in his data
IPS and Cancer
Classifying SNPs
- Can we remove false positives with an algorithm?