Matt:LabNotes/2014-10-9

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Design New Padlock Probe Set for in situ cDNA Capture[edit]

  • 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: 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 [1]
    • Headers look like
 >ENST00000567960 havana:known chromosome:GRCh38:16:90094023:90096189:1 gene:ENSG00000261812 gene_biotype:polymorphic_pseudogene transcript_biotype:polymorphi

c_pseudogene