command_mars.V2.md
DONNEES MARGAUX:
./nextflow src/Mars_seq.nf -c src/Mars_seq.config -profile docker
--fastq "/Volumes/S_OG_2/Sequences/CF18_MP05/R{1,2}_Reads_RUN51.fastq.gz"
--tags "/Volumes/S_OG_2/Sequences/Barcodes/tags3.fa"
--transcriptome "/Volumes/S_OG_2/Sequences/ERCC+Genomes/Mus_musculus.GRCm38.cdna.ercc_Ab.all.fa"
--gtf "/Volumes/S_OG_2/Sequences/ERCC+Genomes/Combined_Mus_musculus_ERCC_Ab.gtf"
--results "results/Mus_musculus_CF18_MP05"
--val 96
DONNEES MARGAUX_reconverted:
./nextflow src/Mars_seq.nf -c src/Mars_seq.config -profile docker
--fastq "/Volumes/S_OG_2/Sequences/CF18_MP05/conversion/Pool_3_Lib_S1_R{1,2}.fastq.gz"
--tags "/Volumes/S_OG_2/Sequences/Barcodes/tags3.fa"
--transcriptome "/Volumes/S_OG_2/Sequences/ERCC+Genomes/Mus_musculus.GRCm38.cdna.ercc_Ab.all.fa"
--gtf "/Volumes/S_OG_2/Sequences/ERCC+Genomes/Combined_Mus_musculus_ERCC_Ab.gtf"
--results "results/Mus_musculus_CF18_MP05_reconverted"
--val 96
DONNEES CAMILLE_reconverted:
./nextflow src/Mars_seq.nf -c src/Mars_seq.config -profile docker
--fastq "/Volumes/S_OG_2/Sequences/CF18_MP05/conversion/Pool_3_Lib_S1_R{1,2}.fastq.gz"
--tags "/Volumes/S_OG_2/Sequences/Barcodes/CCAA.fa"
--transcriptome "/Volumes/S_OG_2/Sequences/ERCC+Genomes/Gallus_gallus.GRCg6a.cdna.ercc.all.fa"
--gtf "/Volumes/S_OG_2/Sequences/ERCC+Genomes/Combined_Gallus_Gallus_ERCC.gtf"
--results "/Volumes/S_OG_2/Sequences/results/CF18_PE"
--val 80
DONNEES MARGAUX_reconverted_single_end:
./nextflow src/Mars_seq.nf -c src/Mars_seq.config -profile docker
-w "/Volumes/S_OG_2/work"
--fastq "/Volumes/S_OG_2/Sequences/CF18_MP05/conversion/Pool_3_Lib_S1_R{1,2}.fastq.gz"
--tags "/Volumes/S_OG_2/Sequences/Barcodes/CCAA.fa"
--transcriptome "/Volumes/S_OG_2/Sequences/ERCC+Genomes/Mus_musculus.GRCm38.cdna.ercc_Ab.all.fa"
--gtf "/Volumes/S_OG_2/Sequences/ERCC+Genomes/Combined_Mus_musculus_ERCC_Ab.gtf"
--results "results/Mus_musculus_CF18_MP05_reconverted_single_end"
--val 80
DDONNEES EV116_single_end:
./nextflow src/Mars_seq.nf -c src/Mars_seq.config -profile docker
-w "/Volumes/S_OG_2/work" -resume
--fastq "/Volumes/S_OG_2/Sequences/EV116/EV116_S1_CF03_S2_R{1,2}.fastq"
--tags "/Volumes/S_OG_2/Sequences/Barcodes/EV116_CF03.fa"
--transcriptome "/Volumes/S_OG_2/Sequences/ERCC+Genomes/Gallus_gallus.GRCg6a.cdna.ercc.all.fa"
--gtf "/Volumes/S_OG_2/Sequences/ERCC+Genomes/Combined_Gallus_Gallus_ERCC.gtf"
--results "/Volumes/S_OG_2/Sequences/results/EV116_single_end"
--val 80
DONNEES CAMILLE_reconverted_single_end:
./nextflow src/Mars_seq.nf -c src/Mars_seq.config -profile docker
-w "/Volumes/S_OG_2/work" -resume
--fastq "/Volumes/S_OG_2/Sequences/CF18_MP05/conversion/Pool_3_Lib_S1_R{1,2}.fastq.gz"
--tags "/Volumes/S_OG_2/Sequences/Barcodes/CCAA.fa"
--transcriptome "/Volumes/S_OG_2/Sequences/ERCC+Genomes/Gallus_gallus.GRCg6a.cdna.ercc.all.fa"
--gtf "/Volumes/S_OG_2/Sequences/ERCC+Genomes/Combined_Gallus_Gallus_ERCC.gtf"
--results "/Volumes/S_OG_2/Sequences/results/CF18_single_end_bis"
--val 80