RNA_velocity

# from sra file to fastq with fastq-dump
wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/3.0.0/sratoolkit.3.0.0-ubuntu64.tar.gz
tar -xvf sratoolkit.3.0.0-ubuntu64.tar.gz
export PATH=/home/ubuntu/sratoolkit.3.0.0-ubuntu64:$PATH
vim .bashrc
source ~/.profile
fastq-dump --split-files --gzip SRR#######

velocyto run10x -m /home/ubuntu/rmsk/mm10_rmsk.gtf ./ /home/ubuntu/cellranger/reference/mouse_mm10/refdata-gex-mm10-2020-A/genes/genes.gtf

cellranger count --id=wt_ctl_PB --fastqs=/home/ubuntu/scRNA_seq/neutrophil/ --sample=Wctl_PB2 --transcriptome=/home/ubuntu/cellranger/reference/mouse_mm10/refdata-gex-mm10-2020-A/


# Droplet based tech
# installation
# https://dropest.readthedocs.io/en/latest/droptag.html

./droptag -c ./configs/indrop_v1_2.xml ~/mydata/SRR5945694_2.fastq.gz ~/mydata/SRR5945694_1.fastq.gz

STAR --genomeDir ~/cellranger/refdata-cellranger-mm10-1.2.0/star/ \
       --readFilesIn SRR5945695_1.fastq.gz.tagged.1.fastq.gz,SRR5945695_1.fastq.gz.tagged.2.fastq.gz,SRR5945695_1.fastq.gz.tagged.3.fastq.gz,SRR5945695_1.fastq.gz.tagged.4.fastq.gz,SRR5945695_1.fastq.gz.tagged.5.fastq.gz,SRR5945695_1.fastq.gz.tagged.6.fastq.gz,SRR5945695_1.fastq.gz.tagged.7.fastq.gz,SRR5945695_1.fastq.gz.tagged.8.fastq.gz \
       --outSAMmultNmax 1 \
       --runThreadN 6 \
       --readNameSeparator space \
       --outSAMunmapped Within \
       --outSAMtype BAM SortedByCoordinate \
       --outFileNamePrefix SRR5945695_1 \
       --readFilesCommand gunzip -c