Our own data alignment and analysis: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Shicheng
>Shicheng
Line 20: Line 20:


=== fastq merge by indx ===
=== fastq merge by indx ===
my @file=glob("*gz");
my %file;
foreach my $file(@file){
my @line=split/\.|_/,$file;
push @{$file{$line[1].$line[3]}},$file;
}
foreach my $id(sort keys %file){
        foreach my $sam(@{$file{$id}}){
                print "$sam\t";
        }
        print "\n";
}
  for i in {01,02,04,05,06,07,09,10,11,12}
  for i in {01,02,04,05,06,07,09,10,11,12}
  do
  do

Revision as of 01:11, 15 September 2016


Transfer data from Genome-miner to TSCC

  • md5 to check the integrity
cd /home/shg047/oasis/mouse/alice/raw
for i in `ls *txt.gz`
do
md5sum $i > $i.md5 &
done 
scp shg047@genome-miner.ucsd.edu:/media/NAS3_volume1/SeqStore2016/130104_SN1001/* ./
for i in `ls *txt.gz`
do
md5sum $i > ~/$i.md5 &
done

fastq merge by indx

my @file=glob("*gz");
my %file;
foreach my $file(@file){
my @line=split/\.|_/,$file;
push @{$file{$line[1].$line[3]}},$file;
}
foreach my $id(sort keys %file){
       foreach my $sam(@{$file{$id}}){
               print "$sam\t";
       }
       print "\n";
}


for i in {01,02,04,05,06,07,09,10,11,12}
do
cat s_*_1_Indx$i.txt.gz > Indx$i.read1.fq.gz &
cat s_*_2_Indx$i.txt.gz > Indx$i.read2.fq.gz &
done

RD90 and L80bp Regions

Trim_galore

bismark alignment

RD>10 Regions