miR数据分析处理流程

1.rename方便后续处理。

2.trim_galore去接头。

#这个软件使用之前要先安装fastqc和cutadapt
ls -d OV*|while read OV; do echo $OV;
trim_galore -q 20 --phred33 --paired -a AGATCGGAAGAGCACACGTCT -a2 GATCGTCGGACTGTAGAACTCTGAAC \
-e 0.01 -o /data/XXXXX/task_OV/01trim/ ${OV}/*_R1.fastq.gz ${OV}/*_R2.fastq.gz>>${OV}.log; done

3.fastqc看去接头情况

fastqc -o /data/XXXXX/task_OV/02fastqc -t 10 *.fq.gz

multiqc -o /data/XXXXX/task_OV/02fastqc/multiqc *_fastqc.zip

4.bwa比对

for(( i=1; i<157; i++ ))
do
  bwa mem /data/XXXXX/WGS/02hg19/chrom.37.fa \
  OV${i}_R1_val_1.fq.gz \
  OV${i}_R2_val_2.fq.gz > /data/XXXXX/task_OV/03bwa/OV${i}.sam
done

5.samtools

#SAM2BAM
for(( i=1; i<157; i++ ))
do
  samtools view -bS OV${i}.sam > /data/XXXXX/task_OV/04samtools/OV${i}.bam
done

#SORT
for(( i=10; i<157; i++ ))
do
  samtools sort OV${i}.bam /data/XXXXX/task_OV/05sorted/OV${i}.sort
done

#INDEX
for(( i=1; i<157; i++ ))
do
  samtools index OV${i}.sort.bam
done

6.bedtools

bedtools multicov -f 0.9 -bams OV{1..157}.sort.bam -bed /data/XXXXX/task_LE-miR/03-2miRSeq/hsa.37note_mature.gff > differmiR.txt

7.delete repeat

sort rowname.txt |uniq -d >repeat.name.txt

#repeat
setwd("C:\\Users\\dell-xps\\Desktop")
repeat.name<-read.table("repeat.name.txt", header=TRUE)
differ <- read.table("differ2.txt", header=TRUE)
rowname <- read.table("rowname.txt", header=TRUE)
j<-NULL
for(i in 1:6708){
  a <- as.vector(repeat.name[i,1])
  h <- 0
  g <- NULL
  for(k in 1:99236){
    b <- as.vector(rowname[k,1])
    if(a==b){
      c <- differ[k,]
      h <- h+c
    }
    g <- cbind(a,h)
    g <- as.vector(g)
  }
  j <- rbind(j,g)
}
write.table(j, "serum.iso.repeat.txt")

repeat.iso<-read.table("repeat.txt", header=TRUE)
differ <- read.table("differ.txt", header=TRUE)
for(i in 1:6708){
  a <- as.vector(repeat.iso[i,1])
  for(k in 1:99236){
    b <- as.vector(differ[k,1])
    if(a==b){
      differ[k,]<-repeat.iso[i,]
    }
  }
}
write.table(differ, "serum.iso.repeat.plus.txt")

8.RPM+QC+NORMALIZATION+COMBAT+TEST（看foldchange）

#RPM
setwd("C:\\User