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:
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:
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
** http://genome-tech.ucsd.edu/LabNotes/upload/5/50/PROBESET_Baylor_RPLCACRD_output_final.txt
** http://genome-tech.ucsd.edu/LabNotes/upload/5/50/PROBESET_Baylor_RPLCACRD_output_final.txt
Line 12: Line 56:
** http://genome-tech.ucsd.edu/LabNotes/upload/1/1b/PROBESET_Baylor_FlyDup936_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
** http://genome-tech.ucsd.edu/LabNotes/upload/9/9d/PROBESET_Baylor_FlyDup901_output_final.txt
** FLYDUP5279 is still running on genome-tech
** http://genome-tech.ucsd.edu/LabNotes/upload/6/65/PROBESET_Baylor_FlyDup5279_output_final.txt
* More details on each probeset will be added shortly
** 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=

Latest revision as of 20:50, 17 September 2009

Navigation[edit]

Probeset Upload[edit]

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';
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';
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[edit]

  • G-A bias? Check, Rob noticed it in his data

IPS and Cancer[edit]

Classifying SNPs[edit]

  • Can we remove false positives with an algorithm?