-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathREDO_rna_seq.bash
86 lines (58 loc) · 11.7 KB
/
REDO_rna_seq.bash
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
ls /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/*/*L001_R1*| perl -pe 's/(.+)L001_R1_001.fastq.gz/cat $1L001_R1_001.fastq.gz $1L002_R1_001.fastq.gz $1L003_R1_001.fastq.gz $1L004_R1_001.fastq.gz \> $1.fastq.gz\n/g'
cat /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh143_1-109826732/sh143-1_S6_L001_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh143_1-109826732/sh143-1_S6_L002_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh143_1-109826732/sh143-1_S6_L003_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh143_1-109826732/sh143-1_S6_L004_R1_001.fastq.gz > /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/fastq/sh143-1_R1.fastq.gz &
cat /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh143_2-109814733/sh143-2_S3_L001_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh143_2-109814733/sh143-2_S3_L002_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh143_2-109814733/sh143-2_S3_L003_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh143_2-109814733/sh143-2_S3_L004_R1_001.fastq.gz > /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/fastq/sh143-2_R1.fastq.gz &
cat /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh143_3-109813729/sh143-3_S9_L001_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh143_3-109813729/sh143-3_S9_L002_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh143_3-109813729/sh143-3_S9_L003_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh143_3-109813729/sh143-3_S9_L004_R1_001.fastq.gz > /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/fastq/sh143-3_R1.fastq.gz &
cat /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh202_1-109818737/sh202-1_S8_L001_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh202_1-109818737/sh202-1_S8_L002_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh202_1-109818737/sh202-1_S8_L003_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh202_1-109818737/sh202-1_S8_L004_R1_001.fastq.gz > /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/fastq/shNT-1_R1.fastq.gz &
cat /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh202_2-109819732/sh202-2_S7_L001_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh202_2-109819732/sh202-2_S7_L002_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh202_2-109819732/sh202-2_S7_L003_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh202_2-109819732/sh202-2_S7_L004_R1_001.fastq.gz > /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/fastq/shNT-2_R1.fastq.gz &
cat /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh202_3-109827732/sh202-3_S5_L001_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh202_3-109827732/sh202-3_S5_L002_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh202_3-109827732/sh202-3_S5_L003_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh202_3-109827732/sh202-3_S5_L004_R1_001.fastq.gz > /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/fastq/shNT-3_R1.fastq.gz &
cat /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_1-109823740/sh400-1_S2_L001_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_1-109823740/sh400-1_S2_L002_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_1-109823740/sh400-1_S2_L003_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_1-109823740/sh400-1_S2_L004_R1_001.fastq.gz > /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/fastq/sh400-1_R1.fastq.gz &
cat /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_2-109815738/sh400-2_S4_L001_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_2-109815738/sh400-2_S4_L002_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_2-109815738/sh400-2_S4_L003_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_2-109815738/sh400-2_S4_L004_R1_001.fastq.gz > /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/fastq/sh400-2_R1.fastq.gz &
cat /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_3-109823741/sh400-3_S1_L001_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_3-109823741/sh400-3_S1_L002_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_3-109823741/sh400-3_S1_L003_R1_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_3-109823741/sh400-3_S1_L004_R1_001.fastq.gz > /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/fastq/sh400-3_R1.fastq.gz &
ls /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/*/*L001_R1*| perl -pe 's/(.+)L001_R1_001.fastq.gz/cat $1L001_R2_001.fastq.gz $1L002_R2_001.fastq.gz $1L003_R2_001.fastq.gz $1L004_R2_001.fastq.gz \n/g'
cat /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh143_1-109826732/sh143-1_S6_L001_R2_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh143_1-109826732/sh143-1_S6_L002_R2_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh143_1-109826732/sh143-1_S6_L003_R2_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh143_1-109826732/sh143-1_S6_L004_R2_001.fastq.gz > /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/fastq/sh143-1_R2.fastq.gz &
cat /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh143_2-109814733/sh143-2_S3_L001_R2_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh143_2-109814733/sh143-2_S3_L002_R2_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh143_2-109814733/sh143-2_S3_L003_R2_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh143_2-109814733/sh143-2_S3_L004_R2_001.fastq.gz > /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/fastq/sh143-2_R2.fastq.gz &
cat /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh143_3-109813729/sh143-3_S9_L001_R2_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh143_3-109813729/sh143-3_S9_L002_R2_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh143_3-109813729/sh143-3_S9_L003_R2_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh143_3-109813729/sh143-3_S9_L004_R2_001.fastq.gz > /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/fastq/sh143-3_R2.fastq.gz &
cat /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_1-109823740/sh400-1_S2_L001_R2_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_1-109823740/sh400-1_S2_L002_R2_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_1-109823740/sh400-1_S2_L003_R2_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_1-109823740/sh400-1_S2_L004_R2_001.fastq.gz > /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_1-109823740/sh400-1_S2_.fastq.gz
cat /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_2-109815738/sh400-2_S4_L001_R2_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_2-109815738/sh400-2_S4_L002_R2_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_2-109815738/sh400-2_S4_L003_R2_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_2-109815738/sh400-2_S4_L004_R2_001.fastq.gz > /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_2-109815738/sh400-2_S4_.fastq.gz
cat /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_3-109823741/sh400-3_S1_L001_R2_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_3-109823741/sh400-3_S1_L002_R2_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_3-109823741/sh400-3_S1_L003_R2_001.fastq.gz /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_3-109823741/sh400-3_S1_L004_R2_001.fastq.gz > /home/oleg/DATA/H2AFV_PROJECT/gsc_543_RNA-seq_raw/sh400_3-109823741/sh400-3_S1_.fastq.gz
#######
ls *L001_R1*| perl -pe 's/(.+)L001_R1_001.fastq.gz/cat $1L001_R1_001.fastq.gz $1L002_R1_001.fastq.gz $1L003_R1_001.fastq.gz $1L004_R1_001.fastq.gz \> $1R1.fastq.gz/g'
cat sh143-1_S6_L001_R1_001.fastq.gz sh143-1_S6_L002_R1_001.fastq.gz sh143-1_S6_L003_R1_001.fastq.gz sh143-1_S6_L004_R1_001.fastq.gz > sh143-1_S6_R1.fastq.gz
cat sh143-2_S3_L001_R1_001.fastq.gz sh143-2_S3_L002_R1_001.fastq.gz sh143-2_S3_L003_R1_001.fastq.gz sh143-2_S3_L004_R1_001.fastq.gz > sh143-2_S3_R1.fastq.gz
cat sh143-3_S9_L001_R1_001.fastq.gz sh143-3_S9_L002_R1_001.fastq.gz sh143-3_S9_L003_R1_001.fastq.gz sh143-3_S9_L004_R1_001.fastq.gz > sh143-3_S9_R1.fastq.gz
cat sh202-1_S8_L001_R1_001.fastq.gz sh202-1_S8_L002_R1_001.fastq.gz sh202-1_S8_L003_R1_001.fastq.gz sh202-1_S8_L004_R1_001.fastq.gz > sh202-1_S8_R1.fastq.gz
cat sh202-2_S7_L001_R1_001.fastq.gz sh202-2_S7_L002_R1_001.fastq.gz sh202-2_S7_L003_R1_001.fastq.gz sh202-2_S7_L004_R1_001.fastq.gz > sh202-2_S7_R1.fastq.gz
cat sh202-3_S5_L001_R1_001.fastq.gz sh202-3_S5_L002_R1_001.fastq.gz sh202-3_S5_L003_R1_001.fastq.gz sh202-3_S5_L004_R1_001.fastq.gz > sh202-3_S5_R1.fastq.gz
cat sh400-1_S2_L001_R1_001.fastq.gz sh400-1_S2_L002_R1_001.fastq.gz sh400-1_S2_L003_R1_001.fastq.gz sh400-1_S2_L004_R1_001.fastq.gz > sh400-1_S2_R1.fastq.gz
cat sh400-2_S4_L001_R1_001.fastq.gz sh400-2_S4_L002_R1_001.fastq.gz sh400-2_S4_L003_R1_001.fastq.gz sh400-2_S4_L004_R1_001.fastq.gz > sh400-2_S4_R1.fastq.gz
cat sh400-3_S1_L001_R1_001.fastq.gz sh400-3_S1_L002_R1_001.fastq.gz sh400-3_S1_L003_R1_001.fastq.gz sh400-3_S1_L004_R1_001.fastq.gz > sh400-3_S1_R1.fastq.gz
ls *L001_R1*| perl -pe 's/(.+)L001_R1_001.fastq.gz/cat $1L001_R2_001.fastq.gz $1L002_R2_001.fastq.gz $1L003_R2_001.fastq.gz $1L004_R2_001.fastq.gz \> $1R2.fastq.gz/g'
cat sh143-1_S6_L001_R2_001.fastq.gz sh143-1_S6_L002_R2_001.fastq.gz sh143-1_S6_L003_R2_001.fastq.gz sh143-1_S6_L004_R2_001.fastq.gz > sh143-1_S6_R2.fastq.gz
cat sh143-2_S3_L001_R2_001.fastq.gz sh143-2_S3_L002_R2_001.fastq.gz sh143-2_S3_L003_R2_001.fastq.gz sh143-2_S3_L004_R2_001.fastq.gz > sh143-2_S3_R2.fastq.gz
cat sh143-3_S9_L001_R2_001.fastq.gz sh143-3_S9_L002_R2_001.fastq.gz sh143-3_S9_L003_R2_001.fastq.gz sh143-3_S9_L004_R2_001.fastq.gz > sh143-3_S9_R2.fastq.gz
cat sh202-1_S8_L001_R2_001.fastq.gz sh202-1_S8_L002_R2_001.fastq.gz sh202-1_S8_L003_R2_001.fastq.gz sh202-1_S8_L004_R2_001.fastq.gz > sh202-1_S8_R2.fastq.gz
cat sh202-2_S7_L001_R2_001.fastq.gz sh202-2_S7_L002_R2_001.fastq.gz sh202-2_S7_L003_R2_001.fastq.gz sh202-2_S7_L004_R2_001.fastq.gz > sh202-2_S7_R2.fastq.gz
cat sh202-3_S5_L001_R2_001.fastq.gz sh202-3_S5_L002_R2_001.fastq.gz sh202-3_S5_L003_R2_001.fastq.gz sh202-3_S5_L004_R2_001.fastq.gz > sh202-3_S5_R2.fastq.gz
cat sh400-1_S2_L001_R2_001.fastq.gz sh400-1_S2_L002_R2_001.fastq.gz sh400-1_S2_L003_R2_001.fastq.gz sh400-1_S2_L004_R2_001.fastq.gz > sh400-1_S2_R2.fastq.gz
cat sh400-2_S4_L001_R2_001.fastq.gz sh400-2_S4_L002_R2_001.fastq.gz sh400-2_S4_L003_R2_001.fastq.gz sh400-2_S4_L004_R2_001.fastq.gz > sh400-2_S4_R2.fastq.gz
cat sh400-3_S1_L001_R2_001.fastq.gz sh400-3_S1_L002_R2_001.fastq.gz sh400-3_S1_L003_R2_001.fastq.gz sh400-3_S1_L004_R2_001.fastq.gz > sh400-3_S1_R2.fastq.gz
###################################################
mv sh143-1_S6_R1.fastq.gz RNA_shH2_I_rep1_R1.fastq.gz
mv sh143-1_S6_R2.fastq.gz RNA_shH2_I_rep1_R2.fastq.gz
mv sh143-2_S3_R1.fastq.gz RNA_shH2_I_rep2_R1.fastq.gz
mv sh143-2_S3_R2.fastq.gz RNA_shH2_I_rep2_R2.fastq.gz
mv sh143-3_S9_R1.fastq.gz RNA_shH2_I_rep3_R1.fastq.gz
mv sh143-3_S9_R2.fastq.gz RNA_shH2_I_rep3_R2.fastq.gz
mv sh202-1_S8_R1.fastq.gz RNA_shNT_rep1_R1.fastq.gz
mv sh202-1_S8_R2.fastq.gz RNA_shNT_rep1_R2.fastq.gz
mv sh202-2_S7_R1.fastq.gz RNA_shNT_rep2_R1.fastq.gz
mv sh202-2_S7_R2.fastq.gz RNA_shNT_rep2_R2.fastq.gz
mv sh202-3_S5_R1.fastq.gz RNA_shNT_rep3_R1.fastq.gz
mv sh202-3_S5_R2.fastq.gz RNA_shNT_rep3_R2.fastq.gz
mv sh400-1_S2_R1.fastq.gz RNA_shH2_II_rep1_R1.fastq.gz
mv sh400-1_S2_R2.fastq.gz RNA_shH2_II_rep1_R2.fastq.gz
mv sh400-2_S4_R1.fastq.gz RNA_shH2_II_rep2_R1.fastq.gz
mv sh400-2_S4_R2.fastq.gz RNA_shH2_II_rep2_R2.fastq.gz
mv sh400-3_S1_R1.fastq.gz RNA_shH2_II_rep3_R1.fastq.gz
mv sh400-3_S1_R2.fastq.gz RNA_shH2_II_rep3_R2.fastq.gz
################################################