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===Constitutive Exon Targets=== *Use TargetFiles from [[Matt:LabNotes/2014-11-1]] run ppDesigner.sh cat outputFile_chr*.txt > outputFile_1gap.txt perl ConvertToZeroGapProbe.pl *7,027 probes successfully designed *5,845 exons *407 genes perl Probes2fasta.pl < outputFile_0gap.txt > outputFile_0gap.fa /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d /home/kunzhang/RNAseq/Data/CommonFiles/refMrna.ndx -f outputFile_0gap.fa -F FA -r ALL > outputFile_0gap_novoalign_refMrna.out & /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d /home/kunzhang/softwares/Novocraft/novocraft/human_g1k_v37 -f outputFile_0gap.fa -F FA -r ALL > outputFile_0gap_novoalign_human_g1k_v37.out & perl CleanupProbelist.pl *5,629 probes *4,735 exons *406 genes perl ConvertProbesHg38_2_BedHg19.pl coverageBed -abam BrainBulkTissueRNA_mappedhg19.sorted.bam -b outputFile_0gap_hg19.bed > outputFile_BrainBulkTissueRNA.cov [[File:20141119_Constitutive_RankOrderProbesOverlapReads.JPG]] perl FilterProbelist_LowReadCounts.pl > outputFile_0gap_10reads.txt perl RevComp_Probes.pl *3,126 probes *2,655 exons *378 genes perl FilterProbelist_LowReadCounts.pl > outputFile_0gap_8reads.txt perl RevComp_Probes.pl *3,403 probes *2,879 exons *390 genes [[File:20141119_Constitutive8reads_ProbesperGene.JPG]] perl FilterProbelist_LowProbesPerGene.pl *Remove probes belonging to genes with <8 probes per gene **Outputs: [[Media:OutputFile_0gap_8reads_8pergene.txt | outputFile_0gap_8reads_8pergene.txt]] & [[Media:OutputFile_0gap_8reads_8pergene_RevComp.txt | outputFile_0gap_8reads_8pergene_RevComp.txt]] *Result: 2,542 probes for 165 genes mv outputFile* newGenes_variableArms_ppDesignerFiles
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