Our own data alignment and analysis

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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

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