[General]
title = GE7209
logfile = rnaseq.log

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

# 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 = Beas2B_H3WT_HA, Beas2B_Parental, Beas2B_H3E97K_HA_Clone19, Beas2B_H3E97K_HA_Clone22, Beas2B_H3E97K_HA_Clone23

# Specify the differential analysis contrasts, separating each pair of samples with ^.
contrasts = Beas2B_Parental^Beas2B_H3WT_HA, Beas2B_H3E97K_HA_Clone19^Beas2B_H3WT_HA, Beas2B_H3E97K_HA_Clone22^Beas2B_H3WT_HA, Beas2B_H3E97K_HA_Clone23^Beas2B_H3WT_HA

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 = GE7209
shortLabel = GE7209
longLabel = GE7209
genome = hg38
sizes = hg38.chrom.sizes
dirname = hub
email = your@email.com
url = https://lichtlab.cancer.ufl.edu/reports/H2B/

[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