-
Notifications
You must be signed in to change notification settings - Fork 0
/
siRNA_coverage_filter.sh
61 lines (48 loc) · 4.09 KB
/
siRNA_coverage_filter.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
#!/bin/bash
#SBATCH --job-name=coverage_filter
#SBATCH --partition=batch
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --constraint=AMD
#SBATCH --time=1:00:00
#SBATCH --mem=50gb
#SBATCH --mail-user=gent.edu
#SBATCH --mail-type=BEGIN,END,NONE,FAIL,REQUEUE#SBATCH --mail-type=BEGIN,END,NONE,FAIL,REQUEUE
awk '{ if ($8 >= 50) { print } }' w-EN.sub.siRNAs.bam.CHH_MRs.cov > w-EN.sub.siRNAs.bam.CHH_MRs.50.cov
awk '{ if ($10 >= 50) { print } }' w-EN.sub.siRNAs.bam.mdr1_DMRs.cov > w-EN.sub.siRNAs.bam.mdr1_DMRs.50.cov
awk '{ if ($10 >= 50) { print } }' w-EN.sub.siRNAs.bam.mdr1_EMRs.cov > w-EN.sub.siRNAs.bam.mdr1_EMRs.50.cov
awk '{ if ($8 >= 50) { print } }' m-EN.sub.siRNAs.bam.CHH_MRs.cov > m-EN.sub.siRNAs.bam.CHH_MRs.50.cov
awk '{ if ($10 >= 50) { print } }' m-EN.sub.siRNAs.bam.mdr1_DMRs.cov > m-EN.sub.siRNAs.bam.mdr1_DMRs.50.cov
awk '{ if ($10 >= 50) { print } }' m-EN.sub.siRNAs.bam.mdr1_EMRs.cov > m-EN.sub.siRNAs.bam.mdr1_EMRs.50.cov
awk '{ if ($8 >= 50) { print } }' w-EM.sub.siRNAs.bam.CHH_MRs.cov > w-EM.sub.siRNAs.bam.CHH_MRs.50.cov
awk '{ if ($10 >= 50) { print } }' w-EM.sub.siRNAs.bam.mdr1_DMRs.cov > w-EM.sub.siRNAs.bam.mdr1_DMRs.50.cov
awk '{ if ($10 >= 50) { print } }' w-EM.sub.siRNAs.bam.mdr1_EMRs.cov > w-EM.sub.siRNAs.bam.mdr1_EMRs.50.cov
awk '{ if ($8 >= 50) { print } }' m-EM.sub.siRNAs.bam.CHH_MRs.cov > m-EM.sub.siRNAs.bam.CHH_MRs.50.cov
awk '{ if ($10 >= 50) { print } }' m-EM.sub.siRNAs.bam.mdr1_DMRs.cov > m-EM.sub.siRNAs.bam.mdr1_DMRs.50.cov
awk '{ if ($10 >= 50) { print } }' m-EM.sub.siRNAs.bam.mdr1_EMRs.cov > m-EM.sub.siRNAs.bam.mdr1_EMRs.50.cov
awk '{ if ($8 >= 50) { print } }' J500s.sub.siRNAs.bam.CHH_MRs.cov > J500s.sub.siRNAs.bam.CHH_MRs.50.cov
awk '{ if ($10 >= 50) { print } }' J500s.sub.siRNAs.bam.mdr1_DMRs.cov > J500s.sub.siRNAs.bam.mdr1_DMRs.50.cov
awk '{ if ($10 >= 50) { print } }' J500s.sub.siRNAs.bam.mdr1_EMRs.cov > J500s.sub.siRNAs.bam.mdr1_EMRs.50.cov
awk '{ if ($8 >= 50) { print } }' J500m.sub.siRNAs.bam.CHH_MRs.cov > J500m.sub.siRNAs.bam.CHH_MRs.50.cov
awk '{ if ($10 >= 50) { print } }' J500m.sub.siRNAs.bam.mdr1_DMRs.cov > J500m.sub.siRNAs.bam.mdr1_DMRs.50.cov
awk '{ if ($10 >= 50) { print } }' J500m.sub.siRNAs.bam.mdr1_EMRs.cov > J500m.sub.siRNAs.bam.mdr1_EMRs.50.cov
awk '{ if ($7 == 0) { print } }' w-EN.sub.siRNAs.bam.CHH_MRs.cov > w-EN.sub.siRNAs.bam.CHH_MRs.0.cov
awk '{ if ($9 == 0) { print } }' w-EN.sub.siRNAs.bam.mdr1_DMRs.cov > w-EN.sub.siRNAs.bam.mdr1_DMRs.0.cov
awk '{ if ($9 == 0) { print } }' w-EN.sub.siRNAs.bam.mdr1_EMRs.cov > w-EN.sub.siRNAs.bam.mdr1_EMRs.0.cov
awk '{ if ($7 == 0) { print } }' m-EN.sub.siRNAs.bam.CHH_MRs.cov > m-EN.sub.siRNAs.bam.CHH_MRs.0.cov
awk '{ if ($9 == 0) { print } }' m-EN.sub.siRNAs.bam.mdr1_DMRs.cov > m-EN.sub.siRNAs.bam.mdr1_DMRs.0.cov
awk '{ if ($9 == 0) { print } }' m-EN.sub.siRNAs.bam.mdr1_EMRs.cov > m-EN.sub.siRNAs.bam.mdr1_EMRs.0.cov
awk '{ if ($7 == 0) { print } }' w-EM.sub.siRNAs.bam.CHH_MRs.cov > w-EM.sub.siRNAs.bam.CHH_MRs.0.cov
awk '{ if ($9 == 0) { print } }' w-EM.sub.siRNAs.bam.mdr1_DMRs.cov > w-EM.sub.siRNAs.bam.mdr1_DMRs.0.cov
awk '{ if ($9 == 0) { print } }' w-EM.sub.siRNAs.bam.mdr1_EMRs.cov > w-EM.sub.siRNAs.bam.mdr1_EMRs.0.cov
awk '{ if ($7 == 0) { print } }' m-EM.sub.siRNAs.bam.CHH_MRs.cov > m-EM.sub.siRNAs.bam.CHH_MRs.0.cov
awk '{ if ($9 == 00) { print } }' m-EM.sub.siRNAs.bam.mdr1_DMRs.cov > m-EM.sub.siRNAs.bam.mdr1_DMRs.0.cov
awk '{ if ($9 == 0) { print } }' m-EM.sub.siRNAs.bam.mdr1_EMRs.cov > m-EM.sub.siRNAs.bam.mdr1_EMRs.0.cov
awk '{ if ($7 == 0) { print } }' J500s.sub.siRNAs.bam.CHH_MRs.cov > J500s.sub.siRNAs.bam.CHH_MRs.0.cov
awk '{ if ($9 == 0) { print } }' J500s.sub.siRNAs.bam.mdr1_DMRs.cov > J500s.sub.siRNAs.bam.mdr1_DMRs.0.cov
awk '{ if ($9 == 0) { print } }' J500s.sub.siRNAs.bam.mdr1_EMRs.cov > J500s.sub.siRNAs.bam.mdr1_EMRs.0.cov
awk '{ if ($7 == 0) { print } }' J500m.sub.siRNAs.bam.CHH_MRs.cov > J500m.sub.siRNAs.bam.CHH_MRs.0.cov
awk '{ if ($9 == 0) { print } }' J500m.sub.siRNAs.bam.mdr1_DMRs.cov > J500m.sub.siRNAs.bam.mdr1_DMRs.0.cov
awk '{ if ($9 == 0) { print } }' J500m.sub.siRNAs.bam.mdr1_EMRs.cov > J500m.sub.siRNAs.bam.mdr1_EMRs.0.cov
wc -l *.sub.siRNAs.*.cov > coverage_counts.txt