生信分析常用脚本（一）

1.计算reads PE长度脚本

01.Cal_PE_Depth.sh

Read_count=`gzip -dc Reads1.fq.gz |wc -l |awk '{print $1/4}'`
echo "read pair count : $Read_count"
average_depth=`expr $Read_count \* 200 / 6000000 `
echo average depth: $average_depth

2.计算reads覆盖度

02.coverage.R

depth<-(1599999*100*2/6e6)
print(depth)
coverage<-ppois(40,lambda=depth,lower=F)
print(coverage)

3. 计算N50

03.Cal_N50.pl

#!/usr/bin/perl
use strict;

my $file = shift;

open (IN,"$file") or die ("can't open the file!\n");
open (OUT,">scaf_sort_length.txt") or die ("can't create the file!\n");

my $total_len = 0;
my $ref_len = 6e6;
my $flag = 1;
my @count_len;
my %scaf_hash;
$/=">";
<IN>;
while(<IN>){
   chomp;
   my ($name,@seq) = split(/\n/,$_);
   my $scafseq = join("",@seq);
   $total_len += length($scafseq);
   my $ID = (split(/\s+/,$name))[0];
   $scaf_hash{$ID}=length($scafseq);
}
my $count = 0;

foreach my $key (sort {$scaf_hash{$b}<=>$scaf_hash{$a}} keys %scaf_hash){
       print OUT "$scaf_hash{$key}\n";
       push(@count_len,$scaf_hash{$key});

}

foreach my $len (@count_len){
    $count += $len;
    if ($count /$total_len >=0.5 && $flag){
      print "N50: $len\n";
      $flag = 0;
   }
   if ($count/$total_len>=0.9){
      print "N90: $len\n";
      last;
   }
}

close IN;
close OUT;

4. 长度累积曲线分布图

04.scaf_acclen_graph.R

data<-read.table("scaf_sort_length.txt",header=F)
len<-data[,1]
head(len)
sum<-0
acclen<-numeric(length(len))
for (i in 1:nrow(data)){
   sum <-sum + len[i];
   acclen[i]<-sum;
}
head(acclen)
pdf("Length.pdf")
plot(x=(1:length(acclen)),y=acclen,xlab="accseq ID",ylab="acclen",type="l",col="blue",main="scaSeq accumulate length grap")
dev.off()