Skip to content
Snippets Groups Projects
Select Git revision
  • master
1 result

command_mars.V2.md

Blame
  • user avatar
    elodie authored
    32e54433
    History
    command_mars.V2.md 3.01 KiB

    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