BarcodeAnalysis_v2_gDNA

Barcode Analysis for barcode_v2 gDNA, based on the original SydShafferLab/BarcodeAnalysis. A general description on how to run this code can be found in this wiki.

At this point, this script has been adapted for gDNA analysis and NOT for 10X barcodes. Please use https://github.com/SydShafferLab/BarcodeAnalysis_v2_10X for 10X analysis.

Please refer to the SydShafferLab/BarcodeAnalysis wiki for how to edit the paths_and_variables.json file. These are the main changes from the original .json file:

1. barcodeSource: keep as "gDNA" only.
2. strtseq and strtseq_revcomp have been edited for barcode_v2.
3. bclen: 20
4. sc_mm: 4
5. starseqMatch: 70
6. spike_in_seqs have been edited for new spike-ins that were made for barcode_v2.

Notes:

1. This code was edited to only process one lane file per sample (i.e. only "_L001"). If you have multiple lane .fastq files per sample, please rename the filenames such that all sample filenames have a unique string before "_L001".