-
Notifications
You must be signed in to change notification settings - Fork 40
/
example.sh
167 lines (131 loc) · 9.6 KB
/
example.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
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
# Examples, starting from raw (unfiltered) bam and calling peaks with spp or MACS2 (for some samples)
WORK_ROOT=/srv/scratch/leepc12/grch38_eval/encodeSponge
DATA_ROOT=/mnt/data/grch38_eval/encodeSponge
CHRSZ=/mnt/data/grch38_eval/hg38.primary.genome.size
SCRIPT=/users/leepc12/code/TF_chipseq_pipeline/chipseq.bds
################################################################# /default ##########################################
# mitra (DONE)
NAME=default/wgEncodeBroadHistoneGm12878H3K27me3
BAM1=${DATA_ROOT}/$NAME/wgEncodeBroadHistoneGm12878H3k27me3StdRawDataRep1.bam
BAM2=${DATA_ROOT}/$NAME/wgEncodeBroadHistoneGm12878H3k27me3StdRawDataRep2.bam
CTL_BAM1=${DATA_ROOT}/$NAME/wgEncodeBroadHistoneGm12878ControlStdRawDataPooled.bam
mkdir -p ${WORK_ROOT}/$NAME; cd ${WORK_ROOT}/$NAME; bds $SCRIPT -bam1 $BAM1 -bam2 $BAM2 -ctl_bam1 ${CTL_BAM1} -chrsz $CHRSZ -rm_chr_from_tag "_" -no_spp
# mitra (DONE)
NAME=default/wgEncodeBroadHistoneGm12878H3K4me3
BAM1=${DATA_ROOT}/$NAME/wgEncodeBroadHistoneGm12878H3k4me3StdRawDataRep1.bam
BAM2=${DATA_ROOT}/$NAME/wgEncodeBroadHistoneGm12878H3k4me3StdRawDataRep2.bam
CTL_BAM1=${DATA_ROOT}/$NAME/wgEncodeBroadHistoneGm12878ControlStdRawDataPooled.bam
mkdir -p ${WORK_ROOT}/$NAME; cd ${WORK_ROOT}/$NAME; bds $SCRIPT -bam1 $BAM1 -bam2 $BAM2 -ctl_bam1 ${CTL_BAM1} -chrsz $CHRSZ -rm_chr_from_tag "_" -no_spp
# mitra (DONE)
NAME=default/wgEncodeBroadHistoneGm12878H3K9me3
BAM1=${DATA_ROOT}/$NAME/wgEncodeBroadHistoneGm12878H3k9me3StdRawDataRep1.bam
BAM2=${DATA_ROOT}/$NAME/wgEncodeBroadHistoneGm12878H3k9me3StdRawDataRep2.bam
CTL_BAM1=${DATA_ROOT}/$NAME/wgEncodeBroadHistoneGm12878ControlStdRawDataPooled.bam
mkdir -p ${WORK_ROOT}/$NAME; cd ${WORK_ROOT}/$NAME; bds $SCRIPT -bam1 $BAM1 -bam2 $BAM2 -ctl_bam1 ${CTL_BAM1} -chrsz $CHRSZ -rm_chr_from_tag "_" -no_spp
############ TF chipseq (default)
ADD="-no_spp"
# nandi
NAME=default/wgEncodeHaibTfbsA549NrsfV0422111Etoh02AlnRep0
BAM1=${DATA_ROOT}/$NAME/wgEncodeHaibTfbsA549NrsfV0422111Etoh02RawDataRep1.bam
BAM2=${DATA_ROOT}/$NAME/wgEncodeHaibTfbsA549NrsfV0422111Etoh02RawDataRep2.bam
CTL_BAM1=${DATA_ROOT}/$NAME/wgEncodeHaibTfbsA549RxlchV0422111Etoh02RawDataRep1.bam
mkdir -p ${WORK_ROOT}/$NAME; cd ${WORK_ROOT}/$NAME; bds $SCRIPT -bam1 $BAM1 -bam2 $BAM2 -ctl_bam1 ${CTL_BAM1} -chrsz $CHRSZ -rm_chr_from_tag "_" -wt_spp 24h $ADD
# nandi
NAME=default/wgEncodeHaibTfbsGm12892Taf1V0416102AlnRep0
BAM1=${DATA_ROOT}/$NAME/wgEncodeHaibTfbsGm12892Taf1V0416102RawDataRep1.bam
BAM2=${DATA_ROOT}/$NAME/wgEncodeHaibTfbsGm12892Taf1V0416102RawDataRep2.bam
CTL_BAM1=${DATA_ROOT}/$NAME/wgEncodeHaibTfbsGm12892RxlchV0416102RawDataRep1.bam
mkdir -p ${WORK_ROOT}/$NAME; cd ${WORK_ROOT}/$NAME; bds $SCRIPT -bam1 $BAM1 -bam2 $BAM2 -ctl_bam1 ${CTL_BAM1} -chrsz $CHRSZ -rm_chr_from_tag "_" -wt_spp 24h $ADD
# nandi
NAME=default/wgEncodeSydhTfbsGm12878Ctcfsc15914c20StdAlnRep0
BAM1=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsGm12878Ctcfsc15914c20StdRawDataRep1.bam
BAM2=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsGm12878Ctcfsc15914c20StdRawDataRep2.bam
CTL_BAM1=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsGm12878InputRawData.bam
mkdir -p ${WORK_ROOT}/$NAME; cd ${WORK_ROOT}/$NAME; bds $SCRIPT -bam1 $BAM1 -bam2 $BAM2 -ctl_bam1 ${CTL_BAM1} -chrsz $CHRSZ -rm_chr_from_tag "_" -wt_spp 24h $ADD
# nandi
NAME=default/wgEncodeSydhTfbsGm12878Rad21IggrabAlnRep0
BAM1=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsGm12878Rad21IggrabRawDataRep1.bam
BAM2=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsGm12878Rad21IggrabRawDataRep2.bam
CTL_BAM1=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsGm12878InputIggrabRawDataPooled.bam
mkdir -p ${WORK_ROOT}/$NAME; cd ${WORK_ROOT}/$NAME; bds $SCRIPT -bam1 $BAM1 -bam2 $BAM2 -ctl_bam1 ${CTL_BAM1} -chrsz $CHRSZ -rm_chr_from_tag "_" -wt_spp 24h $ADD
# wotan
NAME=default/wgEncodeSydhTfbsH1hescSuz12UcdAlnRep0
BAM1=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsH1hescSuz12UcdRawDataRep1.bam
BAM2=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsH1hescSuz12UcdRawDataRep2.bam
CTL_BAM1=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsH1hescInputUcdRawData.bam
mkdir -p ${WORK_ROOT}/$NAME; cd ${WORK_ROOT}/$NAME; bds $SCRIPT -bam1 $BAM1 -bam2 $BAM2 -ctl_bam1 ${CTL_BAM1} -chrsz $CHRSZ -rm_chr_from_tag "_" -wt_spp 24h $ADD
# wotan
NAME=default/wgEncodeSydhTfbsHelas3Brf2StdAlnRep0
BAM1=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsHelas3Brf2RawDataRep1.bam
BAM2=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsHelas3Brf2RawDataRep2.bam
CTL_BAM1=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsHelas3InputRawData.bam
mkdir -p ${WORK_ROOT}/$NAME; cd ${WORK_ROOT}/$NAME; bds $SCRIPT -bam1 $BAM1 -bam2 $BAM2 -ctl_bam1 ${CTL_BAM1} -chrsz $CHRSZ -rm_chr_from_tag "_" -wt_spp 24h $ADD
# wotan
NAME=default/wgEncodeSydhTfbsHelas3JundIggrabAlnRep0
BAM1=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsHelas3JundRabiggRawDataRep1.bam
BAM2=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsHelas3JundRabiggRawDataRep2.bam
CTL_BAM1=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsHelas3RabiggRawDataRep1.bam
mkdir -p ${WORK_ROOT}/$NAME; cd ${WORK_ROOT}/$NAME; bds $SCRIPT -bam1 $BAM1 -bam2 $BAM2 -ctl_bam1 ${CTL_BAM1} -chrsz $CHRSZ -rm_chr_from_tag "_" -wt_spp 24h $ADD
################################################################# /sponge ##########################################
############ histone chipseq (sponge)
# mitra (DONE)
NAME=sponge/wgEncodeBroadHistoneGm12878H3K27me3
BAM1=${DATA_ROOT}/$NAME/wgEncodeBroadHistoneGm12878H3k27me3StdRawDataRep1.bam
BAM2=${DATA_ROOT}/$NAME/wgEncodeBroadHistoneGm12878H3k27me3StdRawDataRep2.bam
CTL_BAM1=${DATA_ROOT}/$NAME/wgEncodeBroadHistoneGm12878ControlStdRawDataPooled.bam
mkdir -p ${WORK_ROOT}/$NAME; cd ${WORK_ROOT}/$NAME; bds $SCRIPT -bam1 $BAM1 -bam2 $BAM2 -ctl_bam1 ${CTL_BAM1} -chrsz $CHRSZ -rm_chr_from_tag "other|ribo|mito|_" -no_spp
# mitra (DONE)
NAME=sponge/wgEncodeBroadHistoneGm12878H3K4me3
BAM1=${DATA_ROOT}/$NAME/wgEncodeBroadHistoneGm12878H3k4me3StdRawDataRep1.bam
BAM2=${DATA_ROOT}/$NAME/wgEncodeBroadHistoneGm12878H3k4me3StdRawDataRep2.bam
CTL_BAM1=${DATA_ROOT}/$NAME/wgEncodeBroadHistoneGm12878ControlStdRawDataPooled.bam
mkdir -p ${WORK_ROOT}/$NAME; cd ${WORK_ROOT}/$NAME; bds $SCRIPT -bam1 $BAM1 -bam2 $BAM2 -ctl_bam1 ${CTL_BAM1} -chrsz $CHRSZ -rm_chr_from_tag "other|ribo|mito|_" -no_spp
# mitra (DONE)
NAME=sponge/wgEncodeBroadHistoneGm12878H3K9me3
BAM1=${DATA_ROOT}/$NAME/wgEncodeBroadHistoneGm12878H3k9me3StdRawDataRep1.bam
BAM2=${DATA_ROOT}/$NAME/wgEncodeBroadHistoneGm12878H3k9me3StdRawDataRep2.bam
CTL_BAM1=${DATA_ROOT}/$NAME/wgEncodeBroadHistoneGm12878ControlStdRawDataPooled.bam
mkdir -p ${WORK_ROOT}/$NAME; cd ${WORK_ROOT}/$NAME; bds $SCRIPT -bam1 $BAM1 -bam2 $BAM2 -ctl_bam1 ${CTL_BAM1} -chrsz $CHRSZ -rm_chr_from_tag "other|ribo|mito|_" 3 -no_spp
############ TF chipseq (sponge)
# wotan
NAME=sponge/wgEncodeHaibTfbsA549NrsfV0422111Etoh02AlnRep0
BAM1=${DATA_ROOT}/$NAME/wgEncodeHaibTfbsA549NrsfV0422111Etoh02RawDataRep1.bam
BAM2=${DATA_ROOT}/$NAME/wgEncodeHaibTfbsA549NrsfV0422111Etoh02RawDataRep2.bam
CTL_BAM1=${DATA_ROOT}/$NAME/wgEncodeHaibTfbsA549RxlchV0422111Etoh02RawDataRep1.bam
mkdir -p ${WORK_ROOT}/$NAME; cd ${WORK_ROOT}/$NAME; bds $SCRIPT -bam1 $BAM1 -bam2 $BAM2 -ctl_bam1 ${CTL_BAM1} -chrsz $CHRSZ -rm_chr_from_tag "other|ribo|mito|_" -wt_spp 24h $ADD
# wotan
NAME=sponge/wgEncodeHaibTfbsGm12892Taf1V0416102AlnRep0
BAM1=${DATA_ROOT}/$NAME/wgEncodeHaibTfbsGm12892Taf1V0416102RawDataRep1.bam
BAM2=${DATA_ROOT}/$NAME/wgEncodeHaibTfbsGm12892Taf1V0416102RawDataRep2.bam
CTL_BAM1=${DATA_ROOT}/$NAME/wgEncodeHaibTfbsGm12892RxlchV0416102RawDataRep1.bam
mkdir -p ${WORK_ROOT}/$NAME; cd ${WORK_ROOT}/$NAME; bds $SCRIPT -bam1 $BAM1 -bam2 $BAM2 -ctl_bam1 ${CTL_BAM1} -chrsz $CHRSZ -rm_chr_from_tag "other|ribo|mito|_" -wt_spp 24h $ADD
# wotan
NAME=sponge/wgEncodeSydhTfbsGm12878Ctcfsc15914c20StdAlnRep0
BAM1=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsGm12878Ctcfsc15914c20StdRawDataRep1.bam
BAM2=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsGm12878Ctcfsc15914c20StdRawDataRep2.bam
CTL_BAM1=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsGm12878InputRawData.bam
mkdir -p ${WORK_ROOT}/$NAME; cd ${WORK_ROOT}/$NAME; bds $SCRIPT -bam1 $BAM1 -bam2 $BAM2 -ctl_bam1 ${CTL_BAM1} -chrsz $CHRSZ -rm_chr_from_tag "other|ribo|mito|_" -wt_spp 24h $ADD
# durga
NAME=sponge/wgEncodeSydhTfbsGm12878Rad21IggrabAlnRep0
BAM1=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsGm12878Rad21IggrabRawDataRep1.bam
BAM2=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsGm12878Rad21IggrabRawDataRep2.bam
CTL_BAM1=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsGm12878InputIggrabRawDataPooled.bam
mkdir -p ${WORK_ROOT}/$NAME; cd ${WORK_ROOT}/$NAME; bds $SCRIPT -bam1 $BAM1 -bam2 $BAM2 -ctl_bam1 ${CTL_BAM1} -chrsz $CHRSZ -rm_chr_from_tag "other|ribo|mito|_" -wt_spp 24h $ADD
# durga
NAME=sponge/wgEncodeSydhTfbsH1hescSuz12UcdAlnRep0
BAM1=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsH1hescSuz12UcdRawDataRep1.bam
BAM2=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsH1hescSuz12UcdRawDataRep2.bam
CTL_BAM1=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsH1hescInputUcdRawData.bam
mkdir -p ${WORK_ROOT}/$NAME; cd ${WORK_ROOT}/$NAME; bds $SCRIPT -bam1 $BAM1 -bam2 $BAM2 -ctl_bam1 ${CTL_BAM1} -chrsz $CHRSZ -rm_chr_from_tag "other|ribo|mito|_" -wt_spp 24h $ADD
# durga
NAME=sponge/wgEncodeSydhTfbsHelas3Brf2StdAlnRep0
BAM1=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsHelas3Brf2RawDataRep1.bam
BAM2=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsHelas3Brf2RawDataRep2.bam
CTL_BAM1=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsHelas3InputRawData.bam
mkdir -p ${WORK_ROOT}/$NAME; cd ${WORK_ROOT}/$NAME; bds $SCRIPT -bam1 $BAM1 -bam2 $BAM2 -ctl_bam1 ${CTL_BAM1} -chrsz $CHRSZ -rm_chr_from_tag "other|ribo|mito|_" -wt_spp 24h $ADD
# durga
NAME=sponge/wgEncodeSydhTfbsHelas3JundIggrabAlnRep0
BAM1=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsHelas3JundRabiggRawDataRep1.bam
BAM2=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsHelas3JundRabiggRawDataRep2.bam
CTL_BAM1=${DATA_ROOT}/$NAME/wgEncodeSydhTfbsHelas3RabiggRawDataRep1.bam
mkdir -p ${WORK_ROOT}/$NAME; cd ${WORK_ROOT}/$NAME; bds $SCRIPT -bam1 $BAM1 -bam2 $BAM2 -ctl_bam1 ${CTL_BAM1} -chrsz $CHRSZ -rm_chr_from_tag "other|ribo|mito|_" -wt_spp 24h $ADD