-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathexon_counts.sh
executable file
·77 lines (38 loc) · 4.78 KB
/
exon_counts.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
#!/bin/bash
#$ -cwd
#Abort on any error,
set -e
cd /PATH_TO/Mp_O/host_nonhost/
# non host
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_nonhost_24h_1.bam Mp_nonhost_24h_1.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_nonhost_24h_2.bam Mp_nonhost_24h_2.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_nonhost_24h_3.bam Mp_nonhost_24h_3.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_nonhost_24h_4.bam Mp_nonhost_24h_4.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_nonhost_24h_5.bam Mp_nonhost_24h_5.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_nonhost_3h_1.bam Mp_nonhost_3h_1.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_nonhost_3h_2.bam Mp_nonhost_3h_2.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_nonhost_3h_3.bam Mp_nonhost_3h_3.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_nonhost_3h_4.bam Mp_nonhost_3h_4.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_nonhost_3h_5.bam Mp_nonhost_3h_5.exon_counts
#host
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_host_24h_1.bam Mp_host_24h_1.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_host_24h_2.bam Mp_host_24h_2.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_host_24h_3.bam Mp_host_24h_3.exon_counts
#art
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_art_24h_1.bam Mp_art_24h_1.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_art_24h_2.bam Mp_art_24h_2.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_art_24h_3.bam Mp_art_24h_3.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_art_24h_4.bam Mp_art_24h_4.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_host_24h_4.bam Mp_host_24h_4.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_art_24h_5.bam Mp_art_24h_5.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_host_24h_5.bam Mp_host_24h_5.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_art_3h_1.bam Mp_art_3h_1.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_host_3h_1.bam Mp_host_3h_1.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_art_3h_2.bam Mp_art_3h_2.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_host_3h_2.bam Mp_host_3h_2.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_art_3h_3.bam Mp_art_3h_3.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_host_3h_3.bam Mp_host_3h_3.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_art_3h_4.bam Mp_art_3h_4.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_host_3h_4.bam Mp_host_3h_4.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_art_3h_5.bam Mp_art_3h_5.exon_counts
python /PATH_TO/scratch/dexseq_count.py --stranded no -p no -f bam -r pos /PATH_TO/Mp_O/host_nonhost/Mp_exons.gff Mp_host_3h_5.bam Mp_host_3h_5.exon_counts