Data S1 - Cell Press

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#are interactive and others require code modification to specify parameters as ... #This script is for 10x sequencing files and will pair barcodes to reads, remove exact .... #Using the plot and a “reasonable” cutoff for reads per cell. ... #This need only be run once and is based on kindly gifted instructions from Shawn Driscoll.
Data S1-Scripts and command line procedures. Related to STAR Methods, Figure 1 and Figure 3. #The following comprise a series of commands and custom scripts used in the generation of expression matrices #for Giraddi et al 2018. They are set apart by the nomenclature “#START Script Name***”, and “END Script #Name****”. They were called from Terminal on a 2.7Ghz, 12-core Mac Pro with 64GB of RAM. Some of them #are interactive and others require code modification to specify parameters as described below. Users may wish to #improve upon these unexceptional scripts to prevent hanging the system by adding safety measures, interrupts and #warnings. #Start Script BarCodeMerger.R*** #This script is for 10x sequencing files and will pair barcodes to reads, remove exact duplicates (i.e. first pass UMI #correction), and split cell codes from UMI's to produce input files for UniqueReadsReparser.R (see below) which #concatenates multiple files and carries out second pass UMI correction. #Before running this script, files will need to be placed in a working folder and variables File1R1, File1R2, #File2R1, File2R2 etc need to be designated to include paths and appropriate pairs of files to merge. #load the read files print("loading first read file") ReadsA