[General]
title = Jianping-CS-NS2161-me2-nodex
logfile = chipseq.log

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

# 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 = RC-W-C-K36m2-2, RC-M-C-K36m2-2

# Specify the differential analysis contrasts, separating each pair of samples with ^.
contrasts = RC-M-C-K36m2-2^RC-W-C-K36m2-2

# False discovery rate
fdr = 0.05

steps = samples, fastqcount.1, trim, fastqcount.2, bowtie, bamcount.1, markdupfast, bamcount.2, merge, bamcov, macs, bamtobigwigfast, frip, multiqc, hub
#stopAt = macs

[Hub]
# Directives for automatic genome browser hub creation.
genome = hg38
sizes = /data/reference/icbr/GRCh38/hg38.chrom.sizes
hubname = hub
shortLabel = NS2161-me2-nodex
longLabel = NS2161-me2-nodex
dirname = NS2161-me2-nodex
url = https://lichtlab.cancer.ufl.edu/reports/NSD2/

[Include]
genome = /data/reference/icbr/GRCh38/GENOMEFILES
fastqs = fastqs.conf