-
Notifications
You must be signed in to change notification settings - Fork 1
/
1_Read quality check and error correct
65 lines (38 loc) · 3.3 KB
/
1_Read quality check and error correct
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
-------------------------------------------------------------------------------------------------------
#Obtain Readfiles
curl -LO https://s3.amazonaws.com/broad_tuco/tuco_hippocampus.1.fq
curl -LO https://s3.amazonaws.com/broad_tuco/tuco_hippocampus.2.fq
curl -LO https://s3.amazonaws.com/broad_tuco/tuco_hypothalamus.1.fq
curl -LO https://s3.amazonaws.com/broad_tuco/tuco_hypothalamus.2.fq
curl -LO https://s3.amazonaws.com/broad_tuco/tuco_liver.1.fq
curl -LO https://s3.amazonaws.com/broad_tuco/tuco_liver.2.fq
curl -LO https://s3.amazonaws.com/broad_tuco/tuco_spleen.1.fq
curl -LO https://s3.amazonaws.com/broad_tuco/tuco_spleen.2.fq
curl -LO https://s3.amazonaws.com/broad_tuco/tuco_ovary.1.fq
curl -LO https://s3.amazonaws.com/broad_tuco/tuco_ovary.2.fq
curl -LO https://s3.amazonaws.com/broad_tuco/tuco_testes.1.fq
curl -LO https://s3.amazonaws.com/broad_tuco/tuco_testes.2.fq
curl -LO https://s3.amazonaws.com/broad_tuco/tuco_skin.1.fq
curl -LO https://s3.amazonaws.com/broad_tuco/tuco_skin.2.fq
curl -LO https://s3.amazonaws.com/broad_tuco/tuco_kidney.1.fq
curl -LO https://s3.amazonaws.com/broad_tuco/tuco_kidney.2.fq
-------------------------------------------------------------------------------------------------------
#Quality check reads
/data/andrew/SolexaQA/SolexaQA++ analysis /data/andrew/reads/tuco_hippocampus.1.fq /data/andrew/reads/tuco_hippocampus.2.fq
/data/andrew/SolexaQA/SolexaQA++ analysis /data/andrew/reads/tuco_hypothalamus.1.fq /data/andrew/reads/tuco_hypothalamus.2.fq
/data/andrew/SolexaQA/SolexaQA++ analysis /data/andrew/reads/tuco_kidney.1.fq /data/andrew/reads/tuco_kidney.2.fq
/data/andrew/SolexaQA/SolexaQA++ analysis /data/andrew/reads/tuco_liver.1.fq /data/andrew/reads/tuco_liver.2.fq
/data/andrew/SolexaQA/SolexaQA++ analysis /data/andrew/reads/tuco_ovary.1.fq /data/andrew/reads/tuco_ovary.2.fq
/data/andrew/SolexaQA/SolexaQA++ analysis /data/andrew/reads/tuco_skin.1.fq /data/andrew/reads/tuco_skin.2.fq
/data/andrew/SolexaQA/SolexaQA++ analysis /data/andrew/reads/tuco_spleen.1.fq /data/andrew/reads/tuco_spleen.2.fq
/data/andrew/SolexaQA/SolexaQA++ analysis /data/andrew/reads/tuco_testes.1.fq /data/andrew/reads/tuco_testes.2.fq
-------------------------------------------------------------------------------------------------------
#Error Correct Reads
perl /opt/Rcorrector/run_rcorrector.pl -t 16 -k 25 -1 /data/andrew/reads/tuco_hippocampus.1.fq -2 /data/andrew/reads/tuco_hippocampus.2.fq
perl /opt/Rcorrector/run_rcorrector.pl -t 16 -k 25 -1 /data/andrew/reads/tuco_hypothalamus.1.fq -2 /data/andrew/reads/tuco_hypothalamus.2.fq
perl /opt/Rcorrector/run_rcorrector.pl -t 16 -k 25 -1 /data/andrew/reads/tuco_kidney.1.fq -2 /data/andrew/reads/tuco_kidney.2.fq
perl /opt/Rcorrector/run_rcorrector.pl -t 16 -k 25 -1 /data/andrew/reads/tuco_liver.1.fq -2 /data/andrew/reads/tuco_liver.2.fq
perl /opt/Rcorrector/run_rcorrector.pl -t 16 -k 25 -1 /data/andrew/reads/tuco_ovary.1.fq -2 /data/andrew/reads/tuco_ovary.2.fq
perl /opt/Rcorrector/run_rcorrector.pl -t 16 -k 25 -1 /data/andrew/reads/tuco_skin.1.fq -2 /data/andrew/reads/tuco_skin.2.fq
perl /opt/Rcorrector/run_rcorrector.pl -t 16 -k 25 -1 /data/andrew/reads/tuco_spleen.1.fq -2 /data/andrew/reads/tuco_spleen.2.fq
perl /opt/Rcorrector/run_rcorrector.pl -t 16 -k 25 -1 /data/andrew/reads/tuco_testes.1.fq -2 /data/andrew/reads/tuco_testes.2.fq