万物开源
转录组质控与组装流程记录
#!/bin/bash
#PBS -N kissplice
#PBS -l nodes=zhangxclab002:ppn=12
#PBS -q batch
#PBS -V
#PBS -S /bin/bash
myPATH="/home/usr/transnp/ncbiraw"
rawdata="/home/usr/transnp/ncbiraw/raw"
fastqdump(){
#注意解压格式：有时候fasterq-dump 不行，必须使用fastq-dump --defline-seq，必须变成下列格式才能放入trinity,不然报错终止：
#@FCC0AWEACXX:6:1101:1424:2187/2
#CCTCTACTTCCCATAAAATCCCATTCTGGATTTCGTTGTAAACAAAAGAGTCGGACAGAAGCTCGTCTCCTGAGAGCAGATCCTGGTAGA
#+URCP.fa.1 FCC0AWEACXX:6:1101:1424:2187 length=90
#CCCFFFFFHHHHHJJJJIJJJJJJJJJJJJJJJJJHJJHJIJJJIJJIJJJIJJJJJJIJIJIJJHHHFFFFFEEEDCEDCDDDDDCCCC
#所以需要使用以下命令
nohup fastq-dump --defline-seq '@$sn[_$rn]/$ri' --split-files URCP.fa &
nohup fastq-dump --defline-seq '@$sn[_$rn]/$ri' --split-files YJJY.fa &
}
fastqc(){
nohup fastqc -t 4 -o ./ URCP.fa_1.fastq URCP.fa_2.fastq &
}
rcorrector(){
nohup ~/miniconda3/envs/py2/bin/run_rcorrector.pl -1 $rawdata/URCP.fa_1.fastq -2 $rawdata/URCP.fa_2.fastq -od ./recorrector &
nohup ~/miniconda3/envs/py2/bin/run_rcorrector.pl -1 $rawdata/YJJY.fa_1.fastq -2 $rawdata/YJJY.fa_2.fastq -od ./recorrector &
}
trimmomatic(){
cd $myPATH
#mkdir ../Trimmomatic
trimmomatic PE -phred33 $myPATH/recorrector/URCP.fa_1.cor.fq $myPATH/recorrector/URCP.fa_2.cor.fq -baseout $myPATH/Trimmomatic/URCP_trim.fq SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:36 &
wait
trimmomatic PE -phred33 $myPATH/recorrector/YJJY.fa_1.cor.fq $myPATH/recorrector/YJJY.fa_2.cor.fq -baseout $myPATH/Trimmomatic/YJJY_trim.fq SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:36 &
wait
}
FastUniq(){
cd $myPATH/trimmomatic
#URCP_trim_1P.fq
#URCP_trim_1P.fq
fastuniq -i $myPATH/trimmomatic/inputU -o $myPATH/fastuniq/URCP_uniq_1.fastq -p ../fastuniq/URCP_uniq_2.fastq &
#YJJY_trim_1P.fq
#YJJY_trim_2P.fq
fastuniq -i $myPATH/trimmomatic/inputY -o $myPATH/fastuniq/YJJY_uniq_1.fastq -p ../fastuniq/YJJY_uniq_2.fastq &
}
fastqc2(){
nohup fastqc -t 4 -o ./ URCP_uniq_1.fastq URCP_uniq_2.fastq &
nohup fastqc -t 4 -o ./ YJJY_uniq_1.fastq YJJY_uniq_2.fastq &
}
trinity(){
cd $myPATH
##conda activate trinity
#nohup Trinity --seqType fq --max_memory 20G --left URCP_uniq_1.fastq --right URCP_uniq_2.fastq --CPU 5 &
nohup /home/usr/miniconda3/envs/trinity/bin/Trinity --seqType fq --max_memory 15G --left $myPATH/fastuniq/URCP_uniq_1.fastq --right $myPATH/fastuniq/URCP_uniq_2.fastq --CPU 5 &
nohup /home/usr/miniconda3/envs/trinity/bin/Trinity --seqType fq --max_memory 15G --left $myPATH/fastuniq/YJJY_uniq_1.fastq --right $myPATH/fastuniq/YJJY_uniq_2.fastq --CPU 5 &
}
wait=`trimmomatic`
wait
FastUniq
编者按：
wait=trimmomatic
wait
是整篇的点睛之笔，实现了function1实现之后function2才启动的流程控制；第一个wait是变量，第二个wait是shell内置函数；具体是赋值变量起作用还是wait函数起作用呢？我觉得双重（bu）比较(zhi)保险(dao)。
隔天更新：由于一个文件夹大小写错了导致wait一直在占用系统，系统变得特别慢直到管理员给我kill。所以请确保程序没有错误再使用wait！ 或者尝试一下新的流程控制，师兄建议我用snakemake.