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