[General]
title = NSD_RS_20230622
logfile = rnaseq.log
seqproject = GE-6783

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

# Link to project page
# project = 

# List the different experimental conditions. Each condition may include multiple
# biological replicates. For example, a wildtype and two different knockouts:
conditions = WT-NSD2i-0, WT-NSD2i-1, Mut-NSD2i-0, Mut-NSD2i-1 

# Specify the differential analysis contrasts, separating each pair of samples with ^.
contrasts = Mut-NSD2i-1^Mut-NSD2i-0, WT-NSD2i-1^WT-NSD2i-0, Mut-NSD2i-1^WT-NSD2i-0

steps = rnasamples, fastqcount.1, trim, fastqcount.2, startx, merge, bamcount, bamcov, rsemquant, deseq, mats, simplediff, bamtobigwigfast, multiqc, methods, hub

[Diff]
fdr = 0.05
fc = 1

[Hub]
# Options in this section are used when generating a UCSC Hub
hubname = NSD_RS_20230622
shortLabel = NSD_RS_20230622
longLabel = NSD_RS_20230622
genome = hg38
sizes = hg38.chrom.sizes
dirname = hub
email = your@email.com
url = https://lichtlab.cancer.ufl.edu/reports/NSD2/

[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