序列质控，clean reads去宿主、去核糖体

for i in 123 98 126 4 128 32 134 8 130 29 131 42 119 19 139 24 125 37 144 14 117 5 142 13 127 22 129 48 138 47 140 20 132 18 149 73 120 105 148 44 122 30 124 26 143 34 133 12 145 21 152 10 118 102 147 80 121 1 151 35 135 38 136 2 150 17 146 55 141 11 137 97
do
bowtie2 -p 80 -x /mnt/database/bowtie/cattle/cattlegenome -1 /mnt/rawdata/dairycow/DNA/clean/$i.clip.1.fq.gz -2 /mnt/rawdata/dairycow/DNA/clean/$i.clip.2.fq.gz --un-conc /mnt/mzy/dairycow/QC/DNA/dehost/$i.fq >tmp.sam
echo dehost is $i.DNA
bowtie2 -p 80 -x /mnt/database/bowtie/SSU/SSU -1 /mnt/mzy/dairycow/QC/DNA/dehost/$i.1.fq -2 /mnt/mzy/dairycow/QC/DNA/dehost/$i.2.fq --un-conc /mnt/mzy/dairycow/QC/DNA/deSSU/$i.fq --al-conc /mnt/mzy/dairycow/rrs/DNA/SSU/$i.fq > /mnt/mzy/dairycow/rrs/DNA/SSU/$i.SSU.sam
echo deSSU is $i.DNA
samtools sort /mnt/mzy/dairycow/rrs/DNA/SSU/$i.SSU.sam|samtools view -bS >/mnt/mzy/dairycow/rrs/DNA/SSU/DNASSU.$i.bam
samtools index /mnt/mzy/dairycow/rrs/DNA/SSU/DNASSU.$i.bam
samtools idxstats /mnt/mzy/dairycow/rrs/DNA/SSU/DNASSU.$i.bam >$i.DNA
rm /mnt/mzy/dairycow/rrs/DNA/SSU/$i.SSU.sam

 

#cd /mnt/mzy/dairycow/sub24/RNA
#for i in 127 134 133 143 140 122 125 117 149 132 130 142 145 152 118 147 121 151 135 136 150 146 141 137
#do
#seqtk sample -s 100 /mnt/mzy/dairycow/QC/RNA/deLSU/$i.1.fq.gz 5000000 > $i.1.fq &
#seqtk sample -s 100 /mnt/mzy/dairycow/QC/RNA/deLSU/$i.2.fq.gz 5000000 > $i.2.fq
#done
#mkdir /mnt/mzy/dairycow/sub24/DNA
cd /mnt/mzy/dairycow/sub24/DNA
for i in 127 134 133 143 140 122 125 117 149 132 130 142 145 152 118 147 121 151 135 136 150 146 141 137
do