#Groupname	Controlname	Replicatename	spikename	email	string_to_identify_sample	string_pair1	string_pair2	nonspecific
iluc197_Rb	NA	rep2	ecoli	ariunaa.bayanjargal@nationwidechildrens.org	iluc197_Rb_rep2	_R1_	_R2_	yes
iluc197_Rb	NA	rep3	ecoli	ariunaa.bayanjargal@nationwidechildrens.org	iluc197_Rb_rep3	_R1_	_R2_	yes
iluc197_K27ac	iluc197_Rb	rep2	ecoli	ariunaa.bayanjargal@nationwidechildrens.org	iluc197_K27ac_rep2	_R1_	_R2_	no
iluc197_K27ac	iluc197_Rb	rep3	ecoli	ariunaa.bayanjargal@nationwidechildrens.org	iluc197_K27ac_rep3	_R1_	_R2_	no
iEF197_Rb	NA	rep2	ecoli	ariunaa.bayanjargal@nationwidechildrens.org	iEF197_Rb_rep2	_R1_	_R2_	yes
iEF197_Rb	NA	rep3	ecoli	ariunaa.bayanjargal@nationwidechildrens.org	iEF197_Rb_rep3	_R1_	_R2_	yes
iEF197_K27ac	iEF197_Rb	rep2	ecoli	ariunaa.bayanjargal@nationwidechildrens.org	iEF197_K27ac_rep2	_R1_	_R2_	no
iEF197_K27ac	iEF197_Rb	rep3	ecoli	ariunaa.bayanjargal@nationwidechildrens.org	iEF197_K27ac_rep3	_R1_	_R2_	no
iEF714_Rb	NA	rep2	ecoli	ariunaa.bayanjargal@nationwidechildrens.org	iEF714_Rb_rep2	_R1_	_R2_	yes
iEF714_Rb	NA	rep3	ecoli	ariunaa.bayanjargal@nationwidechildrens.org	iEF714_Rb_rep3	_R1_	_R2_	yes
iEF714_K27ac	iEF714_Rb	rep2	ecoli	ariunaa.bayanjargal@nationwidechildrens.org	iEF714_K27ac_rep2	_R1_	_R2_	no
iEF714_K27ac	iEF714_Rb	rep3	ecoli	ariunaa.bayanjargal@nationwidechildrens.org	iEF714_K27ac_rep3	_R1_	_R2_	no
iEFDBD_Rb	NA	rep2	ecoli	ariunaa.bayanjargal@nationwidechildrens.org	iEFDBD_Rb_rep2	_R1_	_R2_	yes
iEFDBD_Rb	NA	rep3	ecoli	ariunaa.bayanjargal@nationwidechildrens.org	iEFDBD_Rb_rep3	_R1_	_R2_	yes
iEFDBD_K27ac	iEFDBD_Rb	rep2	ecoli	ariunaa.bayanjargal@nationwidechildrens.org	iEFDBD_K27ac_rep2	_R1_	_R2_	no
iEFDBD_K27ac	iEFDBD_Rb	rep3	ecoli	ariunaa.bayanjargal@nationwidechildrens.org	iEFDBD_K27ac_rep3	_R1_	_R2_	no
iEFDBDp_Rb	NA	rep2	ecoli	ariunaa.bayanjargal@nationwidechildrens.org	iEFDBDp_Rb_rep2	_R1_	_R2_	yes
iEFDBDp_Rb	NA	rep3	ecoli	ariunaa.bayanjargal@nationwidechildrens.org	iEFDBDp_Rb_rep3	_R1_	_R2_	yes
iEFDBDp_K27ac	iEFDBDp_Rb	rep2	ecoli	ariunaa.bayanjargal@nationwidechildrens.org	iEFDBDp_K27ac_rep2	_R1_	_R2_	no
iEFDBDp_K27ac	iEFDBDp_Rb	rep3	ecoli	ariunaa.bayanjargal@nationwidechildrens.org	iEFDBDp_K27ac_rep3	_R1_	_R2_	no
# Do NOT put empty line between this comments and your samples information. i.e. do not put empy line above this line								
# All data must be stored in one """"""""project"""""""" directory with a sub-directory called """"""""fastqs"""""""""""""""								
# containing all the fastq files.								
# you can have sub-directories within your fastq directory								
# Controlname column contains part of the filename for control/background sample.								
# control sample must be control,mock ip, or genomic input samples"""""""""""""""								
# Although you can run the pipeline with two different controls, you cannot have the same sample run with"""""""								
# two different controls. For example: have another iEF-714 with iluc-197 as controlname in addition to the lines above.								
# groupname and controlname must be part of filename								
# groupnames cannot be a substring of each other.								
# For example: iEF-197_copy and iEF-197 as two different groupnames is NOT ALLOWED!!								
# string_to_identify_sample cannot be a substring of each other either.								
# string_to_identify_sample are unique string in the filenames that can be used to identify all the files belonging								
# to the same samples.								
# For example: iEF-714_rep1_L001_R1.fastq.gz, iEF-714_rep1_L002_R1.fastq.gz, iEF-714_rep1_L001_R2.fastq.gz and"""""""								
# iEF-714_rep1_L002_R2.fastq.gz	"are your files for iEF-714 replicate 1, you can use iEF-714_rep1 as"							
# string_to_identify_sample.								
# In this example, controlname for iEF-714 is iEF-197."""""""								
# controlname must be one of groupname, except for iEF-197 which has NA as controlname"""""""								
# replicatename must be part of filename. Replicatename cannot be empty.								
# Even if you only have 1 replicate, please put rep1 as Replicatename."""""""								
# spikename options: ecoli, yeast, and fly. If using other spikename, please put"""""""								
# the fasta file (.fa) in the ref folder inside a new folder. Named this folder and put the folder								
# name as the spikename.								
# nonspecific: yes if sample is control, genomic input, IgG or mock IP sample. Otherwise: no"""""""								
# For example iEF-714_FLAG_S3_rep1.sam will have rep1 as replicatename and iEF-714 as Groupname and iEF-197 as controlname								
# since iEF-714_FLAG_rep1_S3.sam.ecoli is the filename for spike-in, spikename will be ecoli"""""""								
# This file (i.e. samples.txt) needs to be inside the project directory								
# Container only works with fastq.gz input								
# change NA under email column to your email address to get an email when each job is done or when they fail.								
# For more details see README.pdf.								
