比对使用STAR

计算counts使用featureCounts

转化counts使用脚本 readsToTPM.pl

$usage = "perl feartureCounts featureCounts.summary";die  "\t\"the usage is  $usage \"\t " if @ARGV ==0;open FILE,$ARGV[0] or die $!;open FILE2,$ARGV[1] or die $1;open OUT1,">TPM.txt";open OUT2,">reads.txt";print OUT1 "geneName\tTPM\n";print OUT2 "geneName\treadsCount\n";while(){chomp;if ($_ =~ /Assigned\t(\d+)/){$totalReads = $1;last;}}while(){

chomp;

next if $_ =~ /[Program][Geneid]/;

@a = split;

printf OUT1 $a[0]."\t"."%.2f",$a[6]/$a[5]*1000/$totalReads*1000000;

print OUT1 "\n";

print OUT2 "$a[0]\t$a[6]\n";

}