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Combined 10X and barcoding

##general work flow To combine barcodes with 10X we insert transcribable lineage barcodes into cells and then perform 10X on those barcoded cells. 10X will capture the transcribed lineage barcode and attach it's cell barcode to it. From the completed 10X library prep we then use primers to amplify the barcode sequences out of the 10X material keeping both the 10X cell barcode and our lineage barcode in the amplified product. We then do paired end sequencing to capture the 10X barcode (Read1) as well as out barcode (Read2). In the end we have sequencing runs containing the gene expression data of single cells and a sequencing run with all the barcodes. This code allow you to combine these sequencing runs so that you can attribute lineage barcodes to specific cells sequenced in your 10X run. Specifically these scripts take the barcode sequencing run and modifies the R2 files and creates some files needed to run the Feature Barcode Analysis (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/3.1/using/feature-bc-analysis) pipeline written by 10X.

##Data input

-set up virtual environment -download packages -activate environment using: source /home/<username>/BarcodeAnalysis/10xbc/bin/activate

• edit paths and parameters in script
• run scrip by running: python /Path/to/script/PrepBarcodesForCellRanger.py