Examples
March 30, 2021 · View on GitHub
Case 1: Unstranded, Paired-end, Mouse
nextflow run rikenbit/ramdaq -profile docker \
--genome GRCm39_vM26 --local_annot_dir <path to annotation> \
--reads '*_{R1,R2}_001.fastq.gz' --outdir <path to outdir>
Case 2: Stranded, Paired-end, Mouse
nextflow run rikenbit/ramdaq -profile docker \
--genome GRCm39_vM26 --local_annot_dir <path to annotation> \
--stranded fr-firststrand \
--reads '*_{R1,R2}_001.fastq.gz' --outdir <path to outdir>
Case 3: Unstranded, Single-end, Mouse
nextflow run rikenbit/ramdaq -profile docker \
--genome GRCm39_vM26 --local_annot_dir <path to annotation> \
--single_end \
--reads '*_{R1}_001.fastq.gz' --outdir <path to outdir>
Case 4: Stranded, Single-end, Mouse
nextflow run rikenbit/ramdaq -profile docker
--genome GRCm39_vM26 --local_annot_dir <path to annotation> \
--stranded fr-firststrand --single_end \
--reads '*_{R1}_001.fastq.gz' --outdir <path to outdir>
Case 5: Unstranded, Paired-end, Human
nextflow run rikenbit/ramdaq -profile docker \
--genome GRCh38_v37 --local_annot_dir <path to annotation> ＼
--reads '*_{R1,R2}_001.fastq.gz' --outdir <path to outdir>
Case 6: Stranded, Paired-end, Human
nextflow run rikenbit/ramdaq -profile docker \
--genome GRCh38_v37 --local_annot_dir <path to annotation> \
--stranded fr-firststrand \
--reads '*_{R1,R2}_001.fastq.gz' --outdir <path to outdir>
Case 7: Unstranded, Single-end, Human
nextflow run rikenbit/ramdaq -profile docker \
--genome GRCh38_v37 --local_annot_dir <path to annotation> \
--single_end \
--reads '*_{R1}_001.fastq.gz' --outdir <path to outdir>
Case 8: Stranded, Single-end, Human
nextflow run rikenbit/ramdaq -profile docker \
--genome GRCh38_v37 --local_annot_dir <path to annotation> \
--stranded fr-firststrand --single_end \
--reads '*_{R1}_001.fastq.gz' --outdir <path to outdir>