Matt:LabNotes/2016-4-18
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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
- Since 5,569 probes too many for unique barcodes
- Combine human and mouse control genes
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