Matt:LabNotes/2014-10-9: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Mzcai
mNo edit summary
>Mzcai
Line 22: Line 22:
*No matter what I try I keep getting this error
*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.
   Name "main::exon_info_file" used only once: possible typo at ../src/ppDesigner.pl line 24.
cat: /home/mzcai/altRun/src/probe_parameters.pl: No such file or directory
  couldn't parse input file at ../src/ppDesigner.pl line 16.
couldn't parse input file at ../src/ppDesigner.pl line 16.

Revision as of 17:39, 10 October 2014

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: 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.
 couldn't parse input file at ../src/ppDesigner.pl line 16.