/
mapping.pl
24 lines (24 loc) · 1.48 KB
/
mapping.pl
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#!/usr/bin/perl
use FindBin qw($Bin);
use Cwd qw(abs_path);
$fq1=shift;
$fq2=shift;
$dirname=shift;
@out=split /\//,$fq1;
@out2=split /\//,$fq2;
@name=split /_/,$out[-1];
@name2=split /_/,$out2[-1];
@trim_name=split /\./,$out[-1];
@trim_name2= split /\./,$out2[-1];
$dir=abs_path($dirname);
`mkdir -p $dir/$name[0]/Shell`;
open F, ">$dir/$name[0]/Shell/$name[0]\_filter.sh";
print F "#!/bin/bash\n#SBATCH -N 1 -c 16\n";
print F "trim_galore -j 16 --quality 20 --phred33 --stringency 3 --length 35 -o $dir/$name[0] --paired $fq1 $fq2\n";
print F "gunzip $dir/$name[0]/$trim_name[0]\_val_1.fq.gz $dir/$name[0]/$trim_name2[0]\_val_2.fq.gz\n";
print F "bowtie -S --rf -p 16 /home/liujizhou/project/00.DATABASE/rRNA_database/rRNA_database -1 $dir/$name[0]/$trim_name[0]\_val_1.fq -2 $dir/$name[0]/$trim_name2[0]\_val_2.fq --un $dir/$name[0]/$name[0]\_rmrRNA.fq -S $dir/$name[0]/$name[0].rRNA.sam\n";
print F "rm $dir/$name[0]/$name[0].rRNA.sam\n";
print F "STAR --genomeDir /home/liujizhou/workfs/SFTSV-IP/process/Genome/STAR_INDEX --readFilesIn $dir/$name[0]/$name[0]\_rmrRNA_1.fq $dir/$name[0]/$name[0]\_rmrRNA_2.fq --runThreadN 16 --alignIntronMax 100000 --alignMatesGapMax 100000 --outFilterMismatchNmax 20 --outFilterMismatchNoverLmax 0.2 --readFilesCommand cat --outSAMtype BAM SortedByCoordinate --outFileNamePrefix $dir/$name[0]/$name[0].\n";
print F "samtools index -@ 16 $dir/$name[0]/$name[0].Aligned.sortedByCoord.out.bam\n";
print F "rm $dir/$name[0]/$name[0].sam $dir/$name[0]/$name[0]*.fq\n";
close F;