环状RNA高通量测序需要用到的scripts整理

scripts
cd /work_dictionary/script

//wget.sh
#!/bin/sh
#PBS -N wget
#PBS -o wget.stdout
#PBS -e wget.stderr
#PBS -q bigbatch
#PBS -l mem=1gb,walltime=100:00:00,nodes=1:ppn=1

wget -c -i *.csv

//fastq_dump_sample.sh
#!/bin/sh
#PBS -N fasterq_dump_sample
#PBS -o fasterq_dump_sample.stdout
#PBS -e fasterq_dump_sample.stderr
#PBS -q bigbatch
#PBS -l mem=1gb,walltime=100:00:00,nodes=1:ppn=1

inputsoft=
input=
output=

$inputsoft/fastq-dump --split-e --gzip $input/sample -O $output/

//bwa_sample.sh
#!/bin/sh
#PBS -N bwa_sample
#PBS -o bwa_sample.stdout
#PBS -e bwa_sample.stderr
#PBS -q bigbatch
#PBS -l mem=10gb,walltime=100:00:00,nodes=1:ppn=4

index=
input=
output=

bwa mem -T 19 -t 4 $index/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa $input/sample_1.fastq.gz $input/sample_2.fastq.gz > $output/sample.sam

//CIRI2_sample.sh
#!/bin/sh
#PBS -N CIRI2_sample
#PBS -o CIRI2_sample.stdout
#PBS -e CIRI2_sample.stderr
#PBS -q bigbatch
#PBS -l mem=10gb,walltime=100:00:00,nodes=1:ppn=4

index=
inputsoft=
input=
output=

perl $inputsoft/CIRI2.pl -I $input/sample.sam -O $output/sample.ciri 
                         -F $index/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa -A $index/Homo_sapiens.GRCh38.105.gtf 
                         -T 4;

//CIRI_AS_sample.sh
#!/bin/sh
#PBS -N CIRI_AS_sample
#PBS -o CIRI_AS_sample.stdout
#PBS -e CIRI_AS_sample.stderr
#PBS -q bigbatch
#PBS -l mem=10gb,walltime=100:00:00,nodes=1:ppn=4

index=
inputsoft=
input_1=
input_2=
output=

perl $inputsoft/CIRI_AS_v1.2.pl -S $input_1/sample.sam -C $input_2/sample.ciri 
                                -F $index/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa -A $index/Homo_sapiens.GRCh38.105.gtf 
                                -O $output/SRR11939854 
                                -D yes;

//CIRI_pipeline_sample.sh
#!/bin/sh
#PBS -N CIRI_pipeline_sample
#PBS -o CIRI_pipeline_sample.stdout
#PBS -e CIRI_pipeline_sample.stderr
#PBS -q bigbatch
#PBS -l mem=10gb,walltime=100:00:00,nodes=1:ppn=4

index=
inputsoft=
input=
output=

java -jar $inputsoft/CIRI-full.jar Pipeline -1 $input/sample_1.fastq.gz -2 $input/sample_2.fastq.gz 
                                            -r $index/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa -a $index/Homo_sapiens.GRCh38.105.gtf 
                                            -o sample -d $output/sample 
                                            -t 4;

//CIRI_ro1_sample.sh
#!/bin/sh
#PBS -N CIRI_ro1_sample
#PBS -o CIRI_ro1_sample.stdout
#PBS -e CIRI_ro1_sample.stderr
#PBS -q bigbatch
#PBS -l mem=10gb,walltime=100:00:00,nodes=1:ppn=4

inputsoft=
input=
output=

java -jar $inputsoft/CIRI-full.jar RO1 -1 $input/sample_1.fastq.gz -2 $input/sample_2.fastq.gz -o $output/sample

//bwa_mem_ro1_sample.sh
#!/bin/sh
#PBS -N bwa_mem_ro1_sample
#PBS -o bwa_mem_ro1_sample.stdout
#PBS -e bwa_mem_ro1_sample.stderr
#PBS -q bigbatch
#PBS -l mem=10gb,walltime=100:00:00,nodes=1:ppn=4

index=
input=
output=

bwa mem -T 19 -t 4 $index/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa $input/sample_ro1.fq > $output/sample_ro1.sam

//CIRI_ro2_sample.sh
#!/bin/sh
#PBS -N CIRI_ro2_sample
#PBS -o CIRI_ro2_sample.stdout
#PBS -e CIRI_ro2_sample.stderr
#PBS -q bigbatch
#PBS -l mem=10gb,walltime=100:00:00,nodes=1:ppn=4

index=
inputsoft=
input=
output=

java -jar $inputsoft/CIRI-full.jar RO2 -r $index/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa -s $input/sample_ro1.sam -l 150 -o $output/sample

//CIRI_merge_sample.sh
#!/bin/sh
#PBS -N CIRI_merge_sample
#PBS -o CIRI_merge_sample.stdout
#PBS -e CIRI_merge_sample.stderr
#PBS -q bigbatch
#PBS -l mem=10gb,walltime=100:00:00,nodes=1:ppn=4

index=
inputsoft=
input_1=
input_2=
input_3=
output=

java -jar $inputsoft/CIRI-full.jar Merge -a $index/Homo_sapiens.GRCh38.105.gtf 
                                         -c $input_1/sample.ciri 
                                         -as $input_2/sample_jav.list 
                                         -ro $input_3/sample_ro2_info.list 
                                         -o $output/sample 
                                         -r $index/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa

//CIRI_vis_sample.sh
#!/bin/sh
#PBS -N CIRI_vis_sample
#PBS -o CIRI_vis_sample.stdout
#PBS -e CIRI_vis_sample.stderr
#PBS -q bigbatch
#PBS -l mem=10gb,walltime=100:00:00,nodes=1:ppn=4

index=
inputsoft=
input_1=
input_2=
output=

java -jar $inputsoft/CIRI-vis_v1.4.jar -i $input_1/sample_merge_circRNA_detail.anno 
                                       -l $input_2/sample_library_length.list 
                                       -r $index/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa 
                                       -d $output/sample_vis