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==Design New Padlock Probe Set for in situ cDNA Capture== *Rui and Blue determined most important genes for in situ based on clustering analysis [[media:TopDiffExpGenes_1000hNucDataset_09252014.xlsx]] Gene List for Padlock Probes Tab *Took all the HUGO gene names and removed duplicates **377 removed **543 genes remain *Removed MT-RNR1 and MT-ND6 since they are mitochondrial: [[File:20141009_HUGO_Genelist.txt | 541 genes]] *Used Biomart to get base positions on chromosomes **Output: Associated gene name, Chromosome name, Gene Start, Gene End, Strand *Removed genes that were on chromosomes LRG and HSCHR19LRC_... *Added 'chr' in front of chromosome names *Changed strand name from 1/-1 to +/- *Biomart missed 73 genes **Will have to get these genes with Ensembl Gene IDs *Test on chr1 nohup /home/mzcai/scratch/FISSEQ_cDNA_ProbeDesign/src/ppDesigner.pl /home/mzcai/scratch/FISSEQ_cDNA_ProbeDesign/jobFile_chr1.pl > /home/mzcai/scratch/FISSEQ_cDNA_ProbeDesign/outputFile_chr1.txt & *No matter what I try I keep getting this error Name "main::exon_info_file" used only once: possible typo at ../src/ppDesigner.pl line 24. (warning only) couldn't parse input file at ../src/ppDesigner.pl line 16. (error) **Turns out when I copied the ppDesigner src directory to a new directory I had to change the location of NNParamFile in probe_parameters.pl **From now on don't move or copy ppDesigner unless needed to run in parallel /home/dinh/scripts/ppDesigner_v1.1.mod/src *Downloaded cDNA FASTA sequences from [http://uswest.ensembl.org/info/data/ftp/index.html] **Headers look like >ENST00000567960 havana:known chromosome:GRCh38:16:90094023:90096189:1 gene:ENSG00000261812 gene_biotype:polymorphic_pseudogene transcript_biotype:polymorphi c_pseudogene
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