# Organism name (human, mouse, vanderplanki, yeast: Default = human)
mouse
# Type of analysis (with or without correction: Default = without correction)
without_correction
# First sample (expecting the treatment fastq file: Default = treatment.fastq)
B_J1_0_s.fastq
# Nature of sample (BLESS or genomic: Default = BLESS)
bless
# Second sample (expecting the control fastq file: Default = control.fastq)
g_J1_0_s.fastq
# Nature of sample (BLESS or genomic: Default = GENOMIC)
genomic
# If type of analysis is with_correction give samples 3,4,5
sample3.fastq
# Nature of sample 3 (BLESS or genomic: Default = BLESS)
bless
sample4.fastq
# Nature of sample 4 (BLESS or genomic: Default = BLESS)
bless
sample5.fastq
# Nature of sample 5 (BLESS or genomic: Default = BLESS)
bless
# Fragile band data (organism fragile band: Default human ncbi)
fragile_bands_mouse.txt
# Cyto band data (organism cyto band: Default human ncbi)
cyto_bands_mouse.txt
# Output name (name of your output: Default output.txt)
new-res.txt
# resolution windows size (Default : 250)
10250
# Windows advance (Default : 1, in reality windows size +1)
1
# time course analysis rarefication table (table must contain control and treatment for each time point: Default NO) time_course_bless_genomic_j1.txt
NO
# rarefaction if running time course (Defalut : No)
false
# Number of random samples for rarefaction (Default : 20)
20
# Output directory (Default : Bless_results)
Bless_results
# Genome directory (Default : current directory)
/data24TB/store/julesberlin/mouse/mm10
# Genome mappability (Default : current directory)
/data24TB/store/julesberlin/mouse/map_45/
# data files directory (Default : current directory)
"./"
# Use previous mapping (debugging purposes only). Will not run bowtie and use available mapping (Default : false)
false
# telomere correction  (Default : false)
false
# Sequencing quality check using FASTQC (Default : false)
false
# Post mapping quality check using Samstat (Default : false)
false
# Number of threads (Default : 1)
16
#running mode quiet  (Default : true)
true