[General]
title = NSD2_CS_RCHACV_070218_Mohammad
logfile = chipseq.log
project = https://basespace.illumina.com/run/96022930/UTX_CS_ARP_HA_KARPAS_061218_DAPHNE

# If specified, this will be added to each submitted job as a comment
label = JDL-NSD2-CS

# 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 = 2C-EZH2, 2C-H2AK119ub, 2C-H3K27ac, 2C-H3K27me3, 2C-H3K36me2, 2C-NSD2, 9B-EZH2, 9B-H2AK119ub, 9B-H3K27ac, 9B-H3K27me3, 9B-H3K36me2, 9B-NSD2

# Specify the differential analysis contrasts, separating each pair of samples with ^.
contrasts = 2C-EZH2^9B-EZH2, 2C-H2AK119ub^9B-H2AK119ub, 2C-H3K27ac^9B-H3K27ac, 2C-H3K27me3^9B-H3K27me3, 2C-H3K36me2^9B-H3K36me2, 2C-NSD2^9B-NSD2

# False discovery rate
fdr = 0.05

steps = samples, -fastqcount.1, -trim, -fastqcount.2, -bowtie, -bamcount.1, -markdup, -bamcount.2, -merge, -bamcov, -bamtowig, -macs, -tags, -peaks, -diffpeaks, -motifs, -insertsize, -multiqc, hub

[bamtowig]
#scale = 1000

[Hub]
dirname = hub
genome = hg38
#hubname = 
sizes = hg38.chrom.sizes
shortLabel = NSD2_CS_RCHACV_070218
longLabel = NSD2_CS_RCHACV_070218 ChIP-Seq
email = lichtlab.common@gmail.com
url = http://licht:licht@lichtlab.cancer.ufl.edu/reports/NSD2/

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

[2C-EZH2]                                                                                                                                                                                        
samples = RCHACV-2C-EZH2                                                                                                                                                                         
                                                                                                                                                                                                 
[2C-H2AK119ub]                                                                                                                                                                                   
samples = RCHACV-2C-H2AK119ub                                                                                                                                                                    
                                                                                                                                                                                                 
[2C-H3K27ac]                                                                                                                                                                                     
samples = RCHACV-2C-H3K27ac                                                                                                                                                                      
                                                                                                                                                                                                 
[2C-H3K27me3]                                                                                                                                                                                    
samples = RCHACV-2C-H3K27me3                                                                                                                                                                     
                                                                                                                                                                                                 
[2C-H3K36me2]                                                                                                                                                                                    
samples = RCHACV-2C-H3K36me2                                                                                                                                                                     
                                                                                                                                                                                                 
[2C-NSD2]                                                                                                                                                                                        
samples = RCHACV-2C-NSD2                                                                                                                                                                         
                                                                                                                                                                                                 
[9B-EZH2]                                                                                                                                                                                        
samples = RCHACV-9B-EZH2                                                                                                                                                                         
                                                                                                                                                                                                 
[9B-H2AK119ub]                                                                                                                                                                                   
samples = RCHACV-9B-H2AK119ub                                                                                                                                                                    
                                                                                                                                                                                                 
[9B-H3K27ac]                                                                                                                                                                                     
samples = RCHACV-9B-H3K27ac                                                                                                                                                                      
                                                                                                                                                                                                 
[9B-H3K27me3]                                                                                                                                                                                    
samples = RCHACV-9B-H3K27me3                                                                                                                                                                     
                                                                                                                                                                                                 
[9B-H3K36me2]                                                                                                                                                                                    
samples = RCHACV-9B-H3K36me2                                                                                                                                                                     
                                                                                                                                                                                                 
[9B-NSD2]                                                                                                                                                                                        
samples = RCHACV-9B-NSD2