Our own data alignment and analysis

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Revision as of 01:17, 15 September 2016 by >Shicheng (→‎fastq merge by indx)
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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

  • Trim fastq separately
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";
}

perl compile.pl > FastMatch.txt
perl ~/bin/trimGolrePBS.pl FastMatch.txt submit
  • bismark alignment separately


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