inDrop_Processing

Initial processing and mapping indrop data

Getting Started

You will need the demultiplexed fastqs. An example bcl2fastq command is below for this library construction. Barcodes should be specified on the SampleSheet.csv file.

bcl2fastq --runfolder-dir ./Files --sample-sheet ./SampleSheet.csv --output-dir ./ --use-bases-mask y58n*,y*,I*,y16n* --mask-short-adapter-reads 0 --minimum-trimmed-read-length 0 --barcode-mismatches 1

Prerequisites

Nextflow; Python; Samtools; Tophat2

Run the nextflow pipeline

Edit the paths on this script to your local paths

./run_nextflow.sh > ./run_log.txt &