[General]
title = NS3526-noIgG
logfile = cutandrun.log

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

# 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 = 32D-Dnmt3a-FLAG-aH3K27Ac, 32D-Dnmt3a-FLAG-aH3K27m3, 32D-Dnmt3a-FLAG-aH3K36me2, 32D-Dnmt3a-FLAG-aH3K36me3, 32D-Dnmt3a-FLAG-aH3K4me1, 32D-Dnmt3a-FLAG-aH3K4me3, 32D-Dnmt3a-FLAG-aPolII-S2-P

# Specify the differential analysis contrasts, separating each pair of samples with ^.
contrasts = 32D-Dnmt3a-FLAG-aH3K27Ac^32D-Dnmt3a-FLAG-aH3K27m3

# 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 = False
mode = stringent
enhancers = /data/reference/icbr/Enhancers/enhanceratlas.org/3T3-L1_EP.bed

[Hub]
# Directives for automatic genome browser hub creation.
sizes = /data/reference/icbr/mm10/mm10.chrom.sizes
hubname = hub
shortLabel = NS3526
longLabel = 
dirname = NS3526
url = https://bw:bw@lichtlab.cancer.ufl.edu/reports/MDS/

[Include]
# All genome files are listed in a separate conf file
genome = /data/reference/icbr/mm10/GENOMEFILES
# If fastqs are listed in a separate file, use this
fastqs = fastqs-noIgG.conf