Matt:LabNotes/2016-4-18

From ZhangLabWiki
Revision as of 01:22, 20 April 2016 by >Mzcai (Created page with " *Files in Dropbox/GradZhangLab/CA12k_Apr2016 *dcProbe_Sequences.txt **Cycle \t Color \t 20nt Sequence **21 (7x3) total *Use MakeBarcodeSequenceFile.py in Dropbox/PythonScr...")
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search


  • Files in Dropbox/GradZhangLab/CA12k_Apr2016
  • dcProbe_Sequences.txt
    • Cycle \t Color \t 20nt Sequence
    • 21 (7x3) total
  • Use MakeBarcodeSequenceFile.py in Dropbox/PythonScripts/ to make
    • decoding_linkers_5-cycles.txt
    • decoding_linkers_6-cycles.txt


  • CA12k_Apr2016_ControlGenes_OutputFile.py
    • Combine human and mouse control genes
      • First need to make alter gene names so human and mouse are separate and barcodes are assigned appropriately
    • Mouse
      • Since only 85 probes each probe gets own barcode by adding #1-85 to end of gene name (eg. m-Rpl8-85_0)
      • Add "m-" in front of each gene name
    • Human
      • Since 5,569 probes too many for unique barcodes
        • Instead, each gene gets 2 barcodes. One barcode is for highest score probe for that gene. Second barcode is for the other probes of that gene.
        • 191 genes x 2 = 382 barcodes
      • Add "h-" in front of each gene name

perl Probe2padlockFISSEQ_Apr2016_HumanBrain_V4.pl > outputFile_0gap_FULL_HumanBrain_V4.txt perl Probe2padlockFISSEQ_Apr2016_MouseBrain_V7.pl > outputFile_0gap_FULL_MouseBrain_V7.txt perl Probe2padlockFISSEQ_Apr2016_MouseEmbryo_V6.pl > outputFile_0gap_FULL_MouseEmbryo_V6.txt perl Probe2padlockFISSEQ_Apr2016_ControlGenes_V8.pl > outputFile_0gap_FULL_ControlGenes_V8.txt

perl padlock2oligo_order.pl ("CA12k_Apr2016_OligosOrder.txt")

  • Need to modify outputFile_0gap_FULL_* so that some genes, exons, and probes have multiple barcodes