/
02-trimgalore.sh
79 lines (73 loc) · 5.59 KB
/
02-trimgalore.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
78
79
#!/bin/bash
#SBATCH --partition=compute # Queue selection
#SBATCH --job-name=yrv_trimgalore # Job name
#SBATCH --mail-type=ALL # Mail events (BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=yaamini.venkataraman@whoi.edu # Where to send mail
#SBATCH --ntasks=1 # Run a single task
#SBATCH --cpus-per-task=8 # Number of CPU cores per task
#SBATCH --mem=100gb # Job memory request
#SBATCH --time=10:00:00 # Time limit hrs:min:sec
#SBATCH --output=yrv_trimgalore%j.log # Standard output/error
#SBATCH --chdir=/vortexfs1/scratch/yaamini.venkataraman/02-trimgalore # Working directory for this script
#Exit script if any command fails
set -e
#TrimGalore: Remove most abundant sequences and hard trim 10 bp from each end
/vortexfs1/home/yaamini.venkataraman/TrimGalore-0.6.6/trim_galore \
--output_dir /vortexfs1/scratch/yaamini.venkataraman/02-trimgalore \
--paired \
--fastqc_args \
"--outdir /vortexfs1/scratch/yaamini.venkataraman/02-trimgalore \
--threads 28" \
--non_directional \
--rrbs \
--paired \
--path_to_cutadapt /vortexfs1/home/yaamini.venkataraman/miniconda3/bin/cutadapt \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L2_20-N4_1.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L2_20-N4_2.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L2_20-S1_1.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L2_20-S1_2.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L2_20-S3_1.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L2_20-S3_2.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L2_20-S4_1.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L2_20-S4_2.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L2_5-N1_1.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L2_5-N1_2.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L2_5-N2_1.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L2_5-N2_2.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L2_5-S3_1.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L2_5-S3_2.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L2_5-S4_1.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L2_5-S4_2.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L2_OC-S1_1.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L2_OC-S1_2.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L3_20-N2_1.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L3_20-N2_2.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L3_5-N3_1.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L3_5-N3_2.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L3_5-S2_1.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L3_5-S2_2.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L3_OC-N1_1.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L3_OC-N1_2.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L3_OC-N2_1.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L3_OC-N2_2.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L3_OC-N4_1.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L3_OC-N4_2.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L3_OC-N5_1.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L3_OC-N5_2.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L3_OC-S2_1.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L3_OC-S2_2.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L3_OC-S3_1.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L3_OC-S3_2.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L4_20-N1_1.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L4_20-N1_2.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L4_20-S2_1.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L4_20-S2_2.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L4_5-S1_1.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L4_5-S1_2.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L4_OC-S5_1.fq.gz \
/vortexfs1/home/naluru/Killifish/WHOI-Mummichog_RRBS/190626_I114_FCH7TVNBBXY_L4_OC-S5_2.fq.gz
echo TrimGalore complete
#MultiQC
/vortexfs1/home/yaamini.venkataraman/miniconda3/bin/multiqc \
/vortexfs1/scratch/yaamini.venkataraman/02-trimgalore/.
echo MultiQC complete