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====Linker design==== *I wrote a [[Media:get_decoding_linkers.txt|script]] to generate a list of barcoded linker sequences. A total of [[Media:decoding_linkers_8-stages_2-colors.txt|1792 linkers]] were generated using two colors and eight stages. *Since we will start with ~5000 candidate genes, more barcoded is needed. [[Media:get_decoding_linkers_3_colors.txt|For this I increased the number of colors (fluorophores) to 3]]. With only 7 hybridization stages, we can decode [[Media:decoding_linkers_7-stages_3-colors.txt|5040 genes]]. I also added another constrain that each barcode needs a minimal of two colors. The barcodes are also shorter, which gives more flexibility for the design of the common linker.
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