-
Notifications
You must be signed in to change notification settings - Fork 0
/
call_peaks.sh
executable file
·75 lines (65 loc) · 4.1 KB
/
call_peaks.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
#!/usr/bin/env bash
#assuming you have installed MACS2 with conda, first activate the environment
# conda activate MACS2
# macs2 callpeak --treatment results/bam_files/SUM229_pos_DMSO/Aligned.sortedByCoord.out.bam \
# --control results/bam_files/SUM229_pos_input_DMSO_1/Aligned.sortedByCoord.out.bam \
# --outdir results/peak_calling/SUM229_DMSO/ -n DMSO
#
# macs2 callpeak --treatment results/bam_files/SUM229_pos_Bort/Aligned.sortedByCoord.out.bam \
# --control results/bam_files/SUM229_pos_input_DMSO_1/Aligned.sortedByCoord.out.bam \
# --outdir results/peak_calling/SUM229_Bort/ -n Bort
#
# time macs2 callpeak --treatment results/bam_files/SUM229_pos_MK2206/Aligned.sortedByCoord.out.bam \
# --control results/bam_files/SUM229_pos_input_DMSO_1/Aligned.sortedByCoord.out.bam \
# --outdir results/peak_calling/SUM229_MK2206/ -n MK2206
#
# time macs2 callpeak --treatment results/bam_files/SUM229_pos_Tram/Aligned.sortedByCoord.out.bam \
# --control results/bam_files/SUM229_pos_input_DMSO_1/Aligned.sortedByCoord.out.bam \
# --outdir results/peak_calling/SUM229_Tram/ -n Tram
# macs2 callpeak --treatment results/bam_files/SUM229_pos_Bort/Aligned.sortedByCoord.out.bam \
# --control results/bam_files/SUM229_pos_DMSO/Aligned.sortedByCoord.out.bam \
# --outdir results/peak_calling/SUM229_Bort_vs_DMSO/ -n Bort_gain
#
# macs2 callpeak --treatment results/bam_files/SUM229_pos_DMSO/Aligned.sortedByCoord.out.bam \
# --control results/bam_files/SUM229_pos_Bort/Aligned.sortedByCoord.out.bam \
# --outdir results/peak_calling/SUM229_Bort_vs_DMSO/ -n Bort_lost
#
# macs2 callpeak --treatment results/bam_files/SUM229_pos_MK2206/Aligned.sortedByCoord.out.bam \
# --control results/bam_files/SUM229_pos_DMSO/Aligned.sortedByCoord.out.bam \
# --outdir results/peak_calling/SUM229_MK2206_vs_DMSO/ -n MK2206_gain
#
# macs2 callpeak --treatment results/bam_files/SUM229_pos_DMSO/Aligned.sortedByCoord.out.bam \
# --control results/bam_files/SUM229_pos_MK2206/Aligned.sortedByCoord.out.bam \
# --outdir results/peak_calling/SUM229_MK2206_vs_DMSO/ -n MK2206_lost
#
# macs2 callpeak --treatment results/bam_files/SUM229_pos_Tram/Aligned.sortedByCoord.out.bam \
# --control results/bam_files/SUM229_pos_DMSO/Aligned.sortedByCoord.out.bam \
# --outdir results/peak_calling/SUM229_Tram_vs_DMSO/ -n Tram_gain
#
# macs2 callpeak --treatment results/bam_files/SUM229_pos_DMSO/Aligned.sortedByCoord.out.bam \
# --control results/bam_files/SUM229_pos_MK2206/Aligned.sortedByCoord.out.bam \
# --outdir results/peak_calling/SUM229_Tram_vs_DMSO/ -n Tram_lost
macs2 callpeak --treatment results/bam_files/SUM229_pos_Bort/Aligned.sortedByCoord.out.bam \
--control results/bam_files/SUM229_pos_DMSO/Aligned.sortedByCoord.out.bam \
--outdir results/peak_calling/SUM229_Bort_vs_DMSO_Goulet/ -n Bort_gain\
--broad --max-gap 1000
macs2 callpeak --treatment results/bam_files/SUM229_pos_DMSO/Aligned.sortedByCoord.out.bam \
--control results/bam_files/SUM229_pos_Bort/Aligned.sortedByCoord.out.bam \
--outdir results/peak_calling/SUM229_Bort_vs_DMSO_Goulet/ -n Bort_lost \
--broad --max-gap 1000
macs2 callpeak --treatment results/bam_files/SUM229_pos_MK2206/Aligned.sortedByCoord.out.bam \
--control results/bam_files/SUM229_pos_DMSO/Aligned.sortedByCoord.out.bam \
--outdir results/peak_calling/SUM229_MK2206_vs_DMSO_Goulet/ -n MK2206_gain \
--broad --max-gap 1000
macs2 callpeak --treatment results/bam_files/SUM229_pos_DMSO/Aligned.sortedByCoord.out.bam \
--control results/bam_files/SUM229_pos_MK2206/Aligned.sortedByCoord.out.bam \
--outdir results/peak_calling/SUM229_MK2206_vs_DMSO_Goulet/ -n MK2206_lost \
--broad --max-gap 1000
macs2 callpeak --treatment results/bam_files/SUM229_pos_Tram/Aligned.sortedByCoord.out.bam \
--control results/bam_files/SUM229_pos_DMSO/Aligned.sortedByCoord.out.bam \
--outdir results/peak_calling/SUM229_Tram_vs_DMSO_Goulet/ -n Tram_gain \
--broad --max-gap 1000
macs2 callpeak --treatment results/bam_files/SUM229_pos_DMSO/Aligned.sortedByCoord.out.bam \
--control results/bam_files/SUM229_pos_MK2206/Aligned.sortedByCoord.out.bam \
--outdir results/peak_calling/SUM229_Tram_vs_DMSO_Goulet/ -n Tram_lost \
--broad --max-gap 1000