[General]
title = NS3570
logfile = cutandrun.log

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

# 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 = Beas2B-Parental-aH3, Beas2B-Parental-aH3K4me3, Beas2B-Parental-aHA, Beas2B-H3WT-HA-aH3, Beas2B-H3WT-HA-aH3K4me3, Beas2B-H3WT-HA-aHA, Beas2B-H3E97K-HA-Clone19-aH3, Beas2B-H3E97K-HA-Clone19-aH3K4me3, Beas2B-H3E97K-HA-Clone19-aHA, Beas2B-H3E97K-HA-Clone22-aH3, Beas2B-H3E97K-HA-Clone22-aH3K4me3, Beas2B-H3E97K-HA-Clone22-aHA, Beas2B-H3E97K-HA-Clone23-aH3, Beas2B-H3E97K-HA-Clone23-aH3K4me3, Beas2B-H3E97K-HA-Clone23-aHA, Beas2B-H3E97K-HA-Clone19-IgG, Beas2B-H3E97K-HA-Clone22-IgG, Beas2B-H3E97K-HA-Clone23-IgG, Beas2B-H3WT-HA-IgG, Beas2B-Parental-IgG

# Specify the differential analysis contrasts, separating each pair of samples with ^.
contrasts = Beas2B-H3WT-HA-aH3^Beas2B-Parental-aH3, Beas2B-H3E97K-HA-Clone19-aH3^Beas2B-Parental-aH3, Beas2B-H3E97K-HA-Clone22-aH3^Beas2B-Parental-aH3, Beas2B-H3E97K-HA-Clone23-aH3^Beas2B-Parental-aH3, Beas2B-H3WT-HA-aH3K4me3^Beas2B-Parental-aH3K4me3, Beas2B-H3E97K-HA-Clone19-aH3K4me3^Beas2B-Parental-aH3K4me3, Beas2B-H3E97K-HA-Clone22-aH3K4me3^Beas2B-Parental-aH3K4me3, Beas2B-H3E97K-HA-Clone23-aH3K4me3^Beas2B-Parental-aH3K4me3, Beas2B-H3WT-HA-aHA^Beas2B-Parental-aHA, Beas2B-H3E97K-HA-Clone19-aHA^Beas2B-Parental-aHA, Beas2B-H3E97K-HA-Clone22-aHA^Beas2B-Parental-aHA, Beas2B-H3E97K-HA-Clone23-aHA^Beas2B-Parental-aHA, Beas2B-H3E97K-HA-Clone19-aHA^Beas2B-H3WT-HA-aHA, Beas2B-H3E97K-HA-Clone22-aHA^Beas2B-H3WT-HA-aHA, Beas2B-H3E97K-HA-Clone23-aHA^Beas2B-H3WT-HA-aHA, Beas2B-H3E97K-HA-Clone19-aH3^Beas2B-H3WT-HA-aH3, Beas2B-H3E97K-HA-Clone22-aH3^Beas2B-H3WT-HA-aH3, Beas2B-H3E97K-HA-Clone23-aH3^Beas2B-H3WT-HA-aH3, Beas2B-H3E97K-HA-Clone19-aH3K4me3^Beas2B-H3WT-HA-aH3K4me3, Beas2B-H3E97K-HA-Clone22-aH3K4me3^Beas2B-H3WT-HA-aH3K4me3, Beas2B-H3E97K-HA-Clone23-aH3K4me3^Beas2B-H3WT-HA-aH3K4me3

# False discovery rate
fdr = 0.05

steps = samples, -fastqcount.1, -trim, -fastqcount.2, -bowtie, -bamcount.1, -spikein, -markdupfast, -bamcount.2, -merge, -bamcov, seacr, -frip, seacrdiff, -multiqc, hub
#stopAt = fastp

[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 = False
mode = stringent
enhancers = /data/reference/icbr/DATABASES/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 = NS3570
longLabel = 
dirname = NS3570
url = https://bw:bw@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