salmon合成丰度表

cd /mnt/mzy/dairycow/24samples/profile
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
salmon quant -i /mnt/mzy/dairycow/profile/24index -p 20 --libType A -1 /mnt/mzy/dairycow/sub24/DNA/$i.1.fq -2 /mnt/mzy/dairycow/sub24/DNA/$i.2.fq -o $i.quant
mv $i.quant/quant.sf $i.DNA
done

DNA<-c("127","134","133","143","140","122","125","117","149","132","130","142","145","152","118","147","121","151","135","136","150","146","141","137")
read.table("133.DNA",header=T,stringsAsFactors=F,fill=T)->a
b<-a[,1:2]
for (i in DNA){
        read.table(paste("/mnt/mzy/dairycow/24samples/profile/",i,".DNA",sep=""),header=T,stringsAsFactors=F,fill=T)->a
        b[paste(i)]<-a[,4]
}

row.names(b)<-b[,1]
b<-b[,-(1:2)]
b[-which(rowSums(b)==0),]->c
write.csv(c,file="salmonDNA.csv",row.names=T,col.names=T,quote=F)