[General]
title = GE6680
logfile = rnaseq.log

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

# 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 = None0_NuMUG, dNesp_IAA0_NuMUG, dNesp_IAA2_NuMUG, dNesp_IAA8_NuMUG, None24_NuMUG, None_DMSO_NuMUG, IAA24_NuMUG, dNesp_DMSO_NuMUG, dNesp_IAA24_NuMUG

# Specify the differential analysis contrasts, separating each pair of samples with ^.
contrasts = dNesp_IAA0_NuMUG^IAA24_NuMUG, dNesp_IAA2_NuMUG^IAA24_NuMUG, dNesp_IAA8_NuMUG^IAA24_NuMUG, dNesp_IAA24_NuMUG^IAA24_NuMUG, dNesp_DMSO_NuMUG^dNesp_IAA0_NuMUG, None0_NuMUG^dNesp_DMSO_NuMUG, None0_NuMUG^dNesp_IAA0_NuMUG, dNesp_IAA24_NuMUG^dNesp_DMSO_NuMUG, dNesp_IAA24_NuMUG^None0_NuMUG, dNesp_IAA2_NuMUG^dNesp_IAA0_NuMUG, dNesp_IAA8_NuMUG^dNesp_IAA0_NuMUG, dNesp_IAA24_NuMUG^dNesp_IAA0_NuMUG

#dNesp_IAA0_NuMUG^DNESP_IAA24_NuMUG contains non-existent sample or condition DNESP_IAA24_NuMUG

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

[Diff]
fdr = 0.05
fc = 0.58

[Hub]
# Options in this section are used when generating a UCSC Hub
hubname = GE6680
shortLabel = GE6680
longLabel = GE6680
genome = mm10
sizes = mm10.chrom.sizes
dirname = hub
email = your@email.com
url = https://bw:bw@data.rc.ufl.edu/secure/icbr/LLC/

[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.conf