Athurva Gore/LabNotes/2009-8-19: Difference between revisions
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** 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 | ||
** | ** http://genome-tech.ucsd.edu/LabNotes/upload/6/65/PROBESET_Baylor_FlyDup5279_output_final.txt | ||
** Parameters: | ** Parameters: | ||
our $exon_info_file='/Users/ajgore/Software/PPDesign/Jobs/Baylor/SETNAME/FILENAME'; | our $exon_info_file='/Users/ajgore/Software/PPDesign/Jobs/Baylor/SETNAME/FILENAME'; |
Latest revision as of 20:50, 17 September 2009
[edit]
Probeset Upload[edit]
- 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
- http://genome-tech.ucsd.edu/LabNotes/upload/6/65/PROBESET_Baylor_FlyDup5279_output_final.txt
- 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[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?