-
Notifications
You must be signed in to change notification settings - Fork 0
/
genome_mapping.sh
89 lines (57 loc) · 5.54 KB
/
genome_mapping.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
80
81
82
83
84
#!/bin/bash -l
#SBATCH -J micro_map
#SBATCH -N 1
#SBATCH --ntasks-per-node 4
#SBATCH --mem 4gb
#SBATCH -p biology_fast
#SBATCH --time=01:00:00
#SBATCH --mail-type=ALL
#SBATCH [email protected]
module load fastx-toolkit/0.0.14
module load htslib/1.2.1
module load gcc/4.9.4
module load bcftools/1.2
module load fastx-toolkit/0.0.14
module load htslib/1.2.1
module load gcc/4.9.4
module load bcftools/1.2
##########################################################
/home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx &> ./mirPro_results/wt_Control_1.txt
#################################################################
bin/mirpro_feature_pro -i /home/siva/Documents/microRNA_data/TRIMMED/wt_Control_1.sorted.out.bam -t /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf -o ./miRNA
#################################################################
nohup /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt_Control_1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results -s null -a null -q 0 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx >mirpro_scipt.txt
nohup /home/siva/mirPRo.1.1.4/bin/mirpro -i /home/siva/Documents/microRNA_data/TRIMMED/wt_Control_1.fastq -m /home/siva/Documents/microRNA_data/mature_T.fa -p /home/siva/Documents/microRNA_data/hairpin_T.fa -d ./mirPro_results_1 -s null -a null -q 0 --seed 1 --map-detail 1 -v 1 --arm 1 -c 1 --map-len 15 --map-score 60 --5-upstream 3 --3-upstream 3 --5-downstream 3 --3-downstream 3 -n 0 -r 1 --gtf /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf --novel 1 --other null -g /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --index /home/siva/Documents/microRNA_data/ath_tair10.idx &>mirpro_scipt_1.txt
#################################################################
manatee
-i /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq -o /home/siva/Documents/microRNA_data/Manatee -index /home/siva/Documents/microRNA_data/bowtie_index/arabidopsis_genome -genome /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa -annotation /home/siva/Documents/microRNA_data/Arabidopsis_thaliana.TAIR10.42.gtf
################################################################
`exporting oath to bashrc file`
echo 'export PATH=$PATH:/home/siva/perl5/perlbrew/bin' >> ~/.bashrc
echo 'export PATH=$PATH:/home/siva/perl5/perlbrew/perls/perl-5.28.0/bin' >> ~/.bashrc
echo 'export PATH=$PATH:/home/siva/anaconda3/bin' >> ~/.bashrc
echo 'export PATH=$PATH:/home/siva/anaconda3/condabin' >> ~/.bashrc
echo 'export PATH=$PATH:/home/siva/ViennaRNA-2.4.16/bin' >> ~/.bashrc
echo 'export PATH=$PATH:/home/siva/randfold_src' >> ~/.bashrc
echo 'export PATH=$PATH:/home/siva/bowtie' >> ~/.bashrc
###################################################################
**#Step 1: build an index of the genome**
bowtie-build Arabidopsis_thaliana.TAIR10.dna.toplevel.fa bowtie_index/arabidopsis_genome
`#step (optional): converting fastq to fasta format`
seqtk seq -a /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq > /home/siva/Documents/microRNA_data/miRNA/FASTA/wt-Control-1.fa
cat /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1.fastq | awk '{if(NR%4==1) {printf(">%s\n",substr($0,2));} else if(NR%4==2) print;}' > /home/siva/Documents/microRNA_data/miRNA/FASTA/wt-Control-1_1.fa
sed -n '1~4s/^@/>/p;2~4p' /home/siva/Documents/microRNA_data/TRIMMED/wt-Control-1-3.fastq > /home/siva/Documents/microRNA_data/miRNA/FASTA/wt-Control-1_2.fa
**#Step 2: process reads and map them to the genome**
mapper.pl reads.fa -c -j -k TCGTATGCCGTCTTCTGCTTGT -l 18 -m -p cel_cluster -s reads_collapsed.fa -t reads_collapsed_vs_genome.arf -v
mapper.pl TRIMMED/wt-Control-1.fastq -e -h -j -l 18 -m -p bowtie_index/arabidopsis_genome -s Mirdeep_miRNA/wt-Control-1_collapsed.fa -t Mirdeep_miRNA/wt-Control-1_collapsed_vs_genome.arf -v 2> Mirdeep_log/mapper_wt-Control-1.txt
**#Step 3: fast quantitation of reads mapping to known miRBase precursors.**
quantifier.pl -p precursors_ref_this_species.fa -m mature_ref_this_species.fa \ -r reads_collapsed.fa -t cel -y 16_19
quantifier.pl -p precursors.fa -m mature.fa -r reads.fa -s star.fa -y now -t cel
quantifier.pl -p hairpin_T.fa -m mature_T.fa -r Mirdeep_miRNA/wt-Control-1_collapsed.fa -y now -d
**#Step 4: identification of known and novel miRNAs in the deep sequencing data:**
miRDeep2.pl reads_collapsed.fa cel_cluster.fa reads_collapsed_vs_genome.arf mature_ref_this_species.fa mature_ref_other_species.fa precursors_ref_this_species.fa -t C.elegans 2> report.log
$ dos2unix
miRDeep2.pl Mirdeep_miRNA/wt-Control-1_collapsed.fa Arabidopsis_thaliana.TAIR10.dna.toplevel.fa Mirdeep_miRNA/wt-ABA-3_collapsed_vs_genome.arf -d none none none 2> wt-Control-1_report.log
**#Step 5: browse the results.**
results.html
################################################################################