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droprna's Introduction

DropRNA

Prepare

STAR aligner download GRCh38 and build STAR index download GTF and processed Transcrption, Exon position file from 10X cellranger site

Step1: Extract the Cell Barcode

python 00_get_cellbarcode.py ./10X_1.1.fq.gz  ./X10.1.pickle 10X 20 &

Step2: Stats on the Cell Barcode

python 01_cellbarcode_stats.py _config.json ./X10.1.pickle ./X10.1.stats.json 10X 20000 1000 &

Step3: Split the reads of valid Cell Barcodes

python 02_split_barcode.py ./10X_1.1.fq.gz ./10X_1.2.fq.gz  ./X10.1.stats.json ./reads_10x1 10X &

Step4: Star Alignment

Step5: Tagging Reads to Gene Names

Step6: Aggregate the UMI counts and Read counts from a sample to an Matrix

droprna's People

Contributors

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