MYCN.yml 1.58 KB
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# A row defines some features to describe a sample to analyse.
# You can add as many row as you want below each other. Be sure that
# the name of the row is the same as the file name witout extension.

# boolean value to setup sequencing type (paired-end or single-end)
# true or false
paired_end: false

# directory containing fastq files (rawdata)
fastq_folder: "/home/adminxavier/MYCN/SRA293647_MYCN_BE2/fastq/"

# the genome of interest (fasta file)
genome: "/home/adminxavier/CTCF/Ref/genomeindex/genome.fasta"

# corresponding entire genome size
genome_size: 2913022398

# A file containing chromosome sizes (usualy "chrom.sizes" file)
chrom_sizes: "/home/adminxavier/CTCF/Ref/genomeindex/sizes.genome"

# Does the genome is allready indexed with bowtie2 ?
# directory containing indexed genome files or ""
idx: "/home/adminxavier/CTCF/Ref/genomeindex/"

# output folder under results/ directory
project: "SRA293647_MYCN_BE2"

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# FasterDB exons bed file
exons: "/home/adminxavier/CTCF/ChIPster/data/exon_sorted.bed"

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input:
  
  row1:
    # sample must be a string. It corresponds to the name of the sample
    sample: "SRR2229590_MYCN"
    # fastq is the corresponding fastq file, can be compressed as gz file.
    fastq: "SRR2229590_MYCN.fastq.gz"
    # condition
    condition: "SRA293647_MYCN_BE2"
    # type is related to ChIP type: Input or IP
    type: "IP"
    
  row2:
    sample: "SRR2229591_IgG"
    fastq: "SRR2229591_IgG.fastq.gz"
    condition: "SRA293647_MYCN_BE2"
    type: "Input"

  # Under construction:
  # Organism (hg19, GRCH38, HBV...) default hg19 for FasterDB compatibility
  # organism: ""