利用bowtie2和samtools获得reads在基因集上的反贴率

mkdir /mnt/mzy/dairycow/72samples/mag/geneprofile
cd /mnt/mzy/dairycow/72samples/mag/geneprofile
for j 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 -k 50 -p 88 -x /mnt/mzy/dairycow/24samples/mag/geneprofile/db/maggene -1 /data/72sample/sub72/DNA/$j.1.fq -2 /data/72sample/sub72/DNA/$j.2.fq >tmp.sam
samtools sort tmp.sam|samtools view -bS >tmp.bam && rm tmp.sam
samtools index tmp.bam
samtools idxstats tmp.bam >$j.DNA.abd && rm tmp.bam *bai
rm tmp.bam
done

for j in 123 98 126 107 128 32 134 8 130 29 131 42 119 108 139 24 125 37 144 83 117 5 142 74 127 22 129 81 138 99 140 20 132 82 149 73 120 105 148 44 122 101 124 100 143 76 133 12 145 79 152 77 118 102 147 80 121 106 151 104 135 38 136 2 150 78 146 55 141 11 137 97
do
bowtie2 -k 50 -p 88 -x /mnt/mzy/dairycow/24samples/mag/geneprofile/db/maggene -1 /data/72sample/sub72/RNA/$j.1.fq -2 /data/72sample/sub72/RNA/$j.2.fq >tmp.sam
samtools sort tmp.sam|samtools view -bS >tmp.bam && rm tmp.sam
samtools index tmp.bam
samtools idxstats tmp.bam >$j.RNA.abd && rm tmp.bam *bai
rm tmp.bam
done