RNA-seq align

hisat2 align

begining to analysis raw data, you should be clean the fastq data. Here we use the hisat2 software to do this project.

#usr/bin/perl
use strict;
open IN,"sqf.sh";

my %fg;
my @gg;
while () {
print $_;
}

#usr/bin/perl
use strict;
open I,"Homo_sapiens.GRCh38.81.gtf";
open IO,">Homo_sapiens.gtf";

while () {
    chomp;
    my @ss = split/\t/;
    next if($ss[0] =~ m/CHR/);

    my ($a)= (split/ /,$ss[-1])[1];
    my $al = join"\t",@ss[0..(@ss-2)];
     $a =~ s/\"//g;
     $a =~ s/\;//g;
    print IO $al."\t".$a."\n";
    

    # body...
}