Matt:LabNotes/2016-4-18

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Revision as of 07:17, 20 April 2016 by >Mzcai
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  • 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
    • Modify outputFile_0gap_FULL_MouseEmbryo_V6.txt
      • Acta2: each probe has different barcode
 Acta2	Acta2_0	chr19:34241431-34241432	AATCACTTCAACAGAGGAAGGTCCA	64	TATATTCCCAGGCATGGATGGCATC	64	2.715838	C	TATATTCCCAGGCATGGATGGCATCAATCACTTCAACAGAGGAAGGTCCA	B010303	GTCATATCGGTCACTGTTAATCACTTCAACAGAGGAAGGTCCACTTCAGCTTCCCGATATCCGACGGTAGTGT*TCTTGCGTGCGATACGGAGTAACTGCGACCGTCGGCTTACCATGCGATTAACCGCGACTG*AAATATATTCCCAGGCATGGATGGCATCGATCAGGATACACACTACCC
 Acta2	Acta2_0	chr19:34241664-34241665	GCCTCCAGTTCCTTTCCAAATCAT	64	CAACTGTGAACGTTTTGTGGATCAGC	63	2.761038	C	CAACTGTGAACGTTTTGTGGATCAGCGCCTCCAGTTCCTTTCCAAATCAT	B020023	GTCATATCGGTCACTGTTGCCTCCAGTTCCTTTCCAAATCATCTTCAGCTTCCCGATATCCGACGGTAGTGT*AACGGTATTCGGTCGTCATCTACCATTCGCGTGCGATTCCCATGCGATTAACCGCGACTG*AAACAACTGTGAACGTTTTGTGGATCAGCGATCAGGATACACACTACCC
 Acta2	Acta2_1	chr19:34243507-34243508	CATCATGAAGTGTGATATTGACATCA	59	GCATCCACGAAACCACCTATAACAG	64	2.768782	C	GCATCCACGAAACCACCTATAACAGCATCATGAAGTGTGATATTGACATCA	B030031	GTCATATCGGTCACTGTTCATCATGAAGTGTGATATTGACATCACTTCAGCTTCCCGATATCCGACGGTAGTGT*CTGGTTCGGGCGTACCTAACCAGGGATCGGTCGAGTACGCGAGTGTCGCGCAACTTAGCG*AAGCATCCACGAAACCACCTATAACAGGATCAGGATACACACTACCC
 Acta2	Acta2_2	chr19:34245117-34245118	CTGTGCTATGTAGCTCTGGACTTTG	63	GATTGTCCGTGACATCAAGGAGAAG	64	2.760554	C	GATTGTCCGTGACATCAAGGAGAAGCTGTGCTATGTAGCTCTGGACTTTG	B300032	GTCATATCGGTCACTGTTCTGTGCTATGTAGCTCTGGACTTTGCTTCAGCTTCCCGATATCCGACGGTAGTGT*ACGCTACGGAGTACGCCACTCAGGGATCGGTCGAGTACGCACGTCTGCGTACCGGCTTAG*AAAGATTGTCCGTGACATCAAGGAGAAGGATCAGGATACACACTACCC
 Acta2	Acta2_3	chr19:34246264-34246265	TGTGACTCACAACGTGCCTATCTAT	64	GTATTGTGCTGGACTCTGGAGATGG	63	2.744643	C	GTATTGTGCTGGACTCTGGAGATGGTGTGACTCACAACGTGCCTATCTAT	B210020	GTCATATCGGTCACTGTTTGTGACTCACAACGTGCCTATCTATCTTCAGCTTCCCGATATCCGACGGTAGTGT*CGTATCGGTAGTCGCAACGCTCTTGCGTGCGATACGGAGTTACCATTCGCGTGCGATTCC*AAAGTATTGTGCTGGACTCTGGAGATGGGATCAGGATACACACTACCC
 Acta2	Acta2_4	chr19:34246758-34246759	CCATGTATGTGGCTATTCAGGCTG	64	TATGTTTGAGACCTTCAATGTCCCCG	63	2.740051	C	TATGTTTGAGACCTTCAATGTCCCCGCCATGTATGTGGCTATTCAGGCTG	B110020	GTCATATCGGTCACTGTTCCATGTATGTGGCTATTCAGGCTGCTTCAGCTTCCCGATATCCGACGGTAGTGT*TGTATCGCGCTCGATTGGCATCTTGCGTGCGATACGGAGTTACCATTCGCGTGCGATTCC*AAATATGTTTGAGACCTTCAATGTCCCCGGATCAGGATACACACTACCC
 Acta2	Acta2_5	chr19:34248545-34248546	CCCTGAAGAGCATCCGACACTG	63	CTTTCTATAACGAGCTTCGTGTGGC	64	2.661623	C	CTTTCTATAACGAGCTTCGTGTGGCCCCTGAAGAGCATCCGACACTG	B023100	GTCATATCGGTCACTGTTCCCTGAAGAGCATCCGACACTGCTTCAGCTTCCCGATATCCGACGGTAGTGT*AACGGTATTCGGTCGTCATCGACGAACGGTCGAGATTTACGAATTGTCCGCGCTCTACGA*AAAAAACTTTCTATAACGAGCTTCGTGTGGCGATCAGGATACACACTACCC
 Acta2	Acta2_6	chr19:34251822-34251823	GATAGAACACGGCATCATCACCAAC	64	AGGGATCCTGACGCTGAAGTATCC	64	2.693671	C	AGGGATCCTGACGCTGAAGTATCCGATAGAACACGGCATCATCACCAAC	B110030	GTCATATCGGTCACTGTTGATAGAACACGGCATCATCACCAACCTTCAGCTTCCCGATATCCGACGGTAGTGT*TGTATCGCGCTCGATTGGCATCTTGCGTGCGATACGGAGTCAGGGATCGGTCGAGTACGC*AAAAAGGGATCCTGACGCTGAAGTATCCGATCAGGATACACACTACCC
 Acta2	Acta2_7	chr19:34252601-34252602	GTGTGAAGAGGAAGACAGCACAG	64	CTGAGACGCTGCTCCAGCTAT	64	2.541243	C	CTGAGACGCTGCTCCAGCTATGTGTGAAGAGGAAGACAGCACAG	B210002	GTCATATCGGTCACTGTTGTGTGAAGAGGAAGACAGCACAGCTTCAGCTTCCCGATATCCGACGGTAGTGT*CGTATCGGTAGTCGCAACGCTCTTGCGTGCGATACGGAGTACGTCTGCGTACCGGCTTAG*AAAAAAAAACTGAGACGCTGCTCCAGCTATGATCAGGATACACACTACCC