Initial processing and mapping indrop data
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
Nextflow; Python; Samtools; Tophat2
Edit the paths on this script to your local paths
./run_nextflow.sh > ./run_log.txt &