- Pull our docker image from Docker Hub
docker pull stl23/rnaseq:v1.5
2 Run the pipeline
docker run --rm --privileged=true -v /mnt/data/stl/rna_seq/rnaseq/:/scripts -v /mnt/data/stl/rna_seq/test/cleandata/:/inputs -v /mnt/data/stl/rna_seq/test/RNA_results/:/outputs -v /mnt/data/stl/single_cell/refdata-gex-GRCh38-2020-A/:/genomedb stl23/rnaseq:v1.5 bash -c 'cd /outputs/ && python3 /scripts/run_RNAseq_v1.0.py -i /inputs -o /outputs -r /genomedb/fasta/genome.fa -g /genomedb/genes/genes.gtf --samples SRR8075135,SRR8075136,SRR8075137:SRR8075138,SRR8075139,SRR8075140 --groups ctl:case --compare ctl:case --org hsa --readlength 50 --jobs 3 --mthreads 5'
usage: run_RNAseq_v1.0.py [-h] [-i INPUT] [-o OUTPUT] [-r REFERENCE] [-g GTF]
[-v {hg19,hg38}] [--samples SAMPLES]
[--groups GROUPS] [--compare COMPARE] [--merge]
[--readlength READLENGTH] [--script] [--jobs JOBS]
[--mthreads MTHREADS] [--org ORG]
RNAseq pipeline v1.0
General options:
-h, --help show the help and exit
-i INPUT, --input INPUT
The input directory of clean reads
-o OUTPUT, --output OUTPUT
The output directory
-r REFERENCE, --reference REFERENCE
The fasta file of reference
-g GTF, --gtf GTF The gene annotation file of reference,gtf format
-v {hg19,hg38}, --build_version {hg19,hg38}
Human genome build version,if used,do not set -r and
-g
--samples SAMPLES Sample names. The sample names should be accordant
with that in input directorye.g. sample1,sample2,sampl
e3:sample4,sample5,sample6:sample7...a group of
samples should be seperated by comma
--groups GROUPS Group names. Should be consistent with the order of
samples names.e.g. group1:group2:group3...
--compare COMPARE DEG(Differentially Expressed Genes) group pairs.
group1:group2,group1:group3...
--merge Merge novel transcripts with reference gtf file if set
True,otherwise use reference gtf only
--readlength READLENGTH
average read length for alternative splicing by rMATs.
--script Only generate shell scripts
--jobs JOBS The maximum jobs when run in local at the same time
--mthreads MTHREADS Maximum Threads
Enrichment options:
--org ORG Species for GO/KEGG enrichment