-
Notifications
You must be signed in to change notification settings - Fork 12
/
example_config_file.sh
139 lines (96 loc) · 3.36 KB
/
example_config_file.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
##### Config file for ChIA PIPE ####
### 1) Library information
# The name of the sequencing run
# Unique identifier for the library being processed
run="LDK0004-ds"
# Experiment type
# "ChIA-PET"
# "HiChIP"
# "PLAC-seq"
experiment_type="ChIA-PET"
# The type of sequencing run:
# "miseq" - around 30 million reads
# "hiseq" - around 300 million reads
# "pooled" - around 1 billion reads
run_type="miseq"
# The factor for which the IP was performed
ip_factor="RNAPII"
# Cell type
cell_type="Kc167"
# The directory containing the input FASTQ files
data_dir="../fastq/"
# The names of the FASTQ files
r1_fastq="LDK0004-ds_*_R1_*.fastq.gz"
r2_fastq="LDK0004-ds_*_R2_*.fastq.gz"
### 2) Dependency information
# The directory containing the executables for ChIA-PIPE
bin_dir="/projects/encode/chia_pipe"
# The directory of the local install of ChIA-PIPE dependencies
dep_dir="../dep_dir"
# The name of the primary genome
# For example: "hg19", "hg38", "dm3", "mm9", "mm10"
genome="dm3"
# The reference genome FASTA file for aligning the reads
# (The same directory must also contain the BWA index files)
fasta="/projects/ruan-lab/processing/genomes/dm3/dm3.fa"
# The chrom.sizes file from UCSC Genome browser
# for the relevant genome build
chrom_sizes="/projects/ruan-lab/processing/genomes/dm3/dm3.chrom.sizes"
# The BAM file for the ChIP-seq input control
# (Required for spp; not required for macs2)
# If not available, set to "none"
input_control="none"
# The peak-calling algorithm ("macs2" or "spp")
peak_caller="macs2"
# The folder in BASIC browser to which to upload the tracks
basic_folder="New user testing"
# BED file of promoters for annotating loops
promoter_bed_file="none"
# BED file of enhancers for annotating loops
enhancer_bed_file="none"
## 3) Advanced options: how to run the pipeline
# The phased SNP file for allele-specific analysis
# (If not available, set to "none")
snp_file="none"
# How the pipeline should be executed
# true: execute all steps in the pipeline
# false: execute only the step submitted (mostly used for debugging)
all_steps=true
# Should unessential intermediate files be deleted?
# true: delete intermediate files
# false: retain intermediate files (will take up a lot more disk space)
clean=true
# The ChIA-PET Utilities program
main_prog="${bin_dir}/util/cpu-dir/cpu-dir/cpu"
# The Juicer executable
juicer="${bin_dir}/util/juicer_tools.1.7.5_linux_x64_jcuda.0.8.jar"
# The number of threads to use on the HPC
n_thread=20
# The amount of memory to use on the HPC (in GB)
mem=60
## 4) Expert options: detailed parameters
# The bridge linker sequence used during ChIA-PET
linker_a="ACGCGATATCTTATCTGACT"
# The second half linker sequence (if two linker sequences were used)
linker_b="none"
# The minimum tag length required for aligning to the reference
# genome after linker filtering
min_tag_len=18
# The span threshold for calling an interaction as
#self-ligation vs inter-ligation
self_bp=8000
# The tag extension length during loop clustering
exten_bp=500
# The Z-score threshold for peak calling with SPP
z_thresh=6
# The name of the genetic cross if working with a hybrid strain
hybrid="none"
### 5) Uncomment below to module load dependencies
# module load pigz
# module load java/1.7.0
# module load perl/5.26.0
# module load bedtools/2.26.0
# module load samtools/1.5
# module load R/3.2.1
# module load MACS/2.1.0.20151222
###