[General]
title = H2B_CR_20230613
logfile = cutandrun.log
seqproject = NS-3311

# If specified, this will be added to each submitted job as a comment
label = KP

# Specify non-standard adapters for trimmomatic, if necessary
adapter = NexteraPE-PE.fa

# List the different experimental conditions. Each condition may include multiple
# biological replicates. For example, a wildtype and two different knockouts:
conditions = WT-H3K27ac, HET-H3K27ac, WT-H3K27me3, HET-H3K27me3, WT-H3K4me3, HET-H3K4me3, WT-HA, HET-HA

# Specify the differential analysis contrasts, separating each pair of samples with ^.
contrasts = HET-H3K27ac^WT-H3K27ac, HET-H3K27me3^WT-H3K27me3, HET-H3K4me3^WT-H3K4me3, HET-HA^WT-HA

# False discovery rate
fdr = 0.05

steps = samples, fastqcount.1, trim, fastqcount.2, bowtie, bamcount.1, markdupfast, bamcount.2, merge, bamcov, seacr, frip, seacrdiff, multiqc, hub

[Spikeins]
spikeidx = /data/reference/icbr/bacteria/Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/Bowtie2Index/genome
scalebam = False

[SEACR]
topfrac = 0.05
norm = True
mode = stringent
#enhancers = /data/reference/icbr/Enhancers/enhanceratlas.org/3T3-L1_EP.bed

[Hub]
# Directives for automatic genome browser hub creation.
genome = hg38
sizes = /data/reference/icbr/GRCh38/hg38.chrom.sizes
hubname = hub
shortLabel = H2B_CR_20230613
longLabel = 
dirname = H2B_CR_20230613
url = https://lichtlab.cancer.ufl.edu/reports/H2B/

[Include]
# All genome files are listed in a separate conf file
genome = /data/reference/icbr/GRCh38/GENOMEFILES
# If fastqs are listed in a separate file, use this
fastqs = fastqs.conf