Matt:LabNotes/2014-10-9: Difference between revisions
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*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. | ||
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.