转录组专题：sra预处理

gencode.v27.annotation

#!/bin/bash
for sj in SRR5938434
do
  fastq-dump --split-3 /run/media/root/NETAC/SRP115571/${sj}.sra --outdir /root/fastq
  fastx_trimmer -v -f1 -l95 -i /root/fastq/${sj}_1.fastq -o /root/fastq/${sj}_g_1.fastq
  fastx_trimmer -v -f1 -l95 -i /root/fastq/${sj}_2.fastq -o /root/fastq/${sj}_g_2.fastq
  fastqc -f fastq -o /root/fastqc /root/fastq/${sj}_g_1.fastq
  fastqc -f fastq -o /root/fastqc /root/fastq/${sj}_g_2.fastq
  sleep 5
  hisat2 --known-splicesite-infile /root/gencode.v27.annotation.ss -p 4 --dta -x /root/gh38_index/index -1 /root/fastq/${sj}_g_1.fastq -2 /root/fastq/${sj}_g_2.fastq -S /root/sam/${sj}.sam -t
   sleep 5
  samtools view -bS /root/sam/${sj}.sam>/root/bam/${sj}.bam
  samtools sort -l1 -T /root/PREFIX /root/bam/${sj}.bam -o /root/bam/${sj}_sorted.bam
   sleep 5
  mkdir /root/gtf/${sj}
  stringtie /root/bam/${sj}_sorted.bam -p4 -e -G /root/gtf/gencode.v27.annotation.gtf -B -o /root/gtf/${sj}/${sj}.gtf -A /root/gtf/${sj}/${sj}_gene_abund.tab
  rm /root/fastq/${sj}_1.fastq
  rm /root/fastq/${sj}_2.fastq
  rm /root/fastq/${sj}_g_1.fastq
  rm /root/fastq/${sj}_g_2.fastq
  rm /root/sam/${sj}.sam
  rm /root/bam/${sj}.bam
  rm /root/bam/${sj}_sorted.bam
done

prepDE.py

fastq-dump --split-3 /run/media/root/NETAC/SRP115571/SRR5938419.sra --outdir /root/fastq --bzip2
bunzip2 FileName.bz2 -k 
bzip2 -z FileName.bz2
rm -f aaa_*.txt
perl fastqc -f fastq -o /root/fastqc /root/fastq/SRR5938419_1.fastq
perl fastqc -f fastq -o /root/fastqc /root/fastq/SRR5938419_2.fastq
fastx_trimmer -v -f10 -l100 -i /root/fastq/SRR5938419_1.fastq -o /root/fastq/SRR5938419_tr_1.fastq
fastx_trimmer -v -f10 -l100 -i /root/fastq/SRR5938419_2.fastq -o /root/fastq/SRR5938419_tr_2.fastq
perl fastqc -f fastq -o /root/fastqc /root/fastq/SRR5938419_tr_1.fastq
perl fastqc -f fastq -o /root/fastqc /root/fastq/SRR5938419_tr_2.fastq
perl hisat2 --known-splicesite-infile /root/gencode.v27.annotation.ss -p 4 --dta -t -x /root/gh38_index/index -1 /root/fastq/SRR5938419_1.fastq -2 /root/fastq/SRR5938419_2.fastq -S /root/sam/SRR5938419.sam
perl hisat2  --known-splicesite-infile /root/gencode.v27.annotation.ss -p 4 --dta  -x /root/gh38_index/index -1 /root/fastq/SRR5938419_1.fastq -2 /root/fastq/SRR5938419_2.fastq -S /root/sam/SRR5938419.sam  -t
samtools view -bS /root/sam/SRR5938419.sam>/root/bam/SRR5938419.bam
samtools sort -l1 -T /root/PREFIX /root/bam/SRR5938419.bam -o /root/bam/SRR593841_sorted.bam
samtools view -h /root/bam/SRR593841.sorted.bam | perl -ne 'if(/HI:i:(d+)/) {$m=$1-1; $_ =~ s/HI:i:(d+)/HI:i:$m/} print $_;'| samtools view -bS /root/bam/SRR593841.sorted.bam > /root/bam/SRR593841.correct.bam
stringtie /root/bam/SRR593841_bam -p4 -e -G /root/gtf/gencode.v27.annotation.gtf -B -o /root/gtf/SRR593841.gtf
python prepDE.py -i /root/count_matrix -g /root/count_matrix/gene_count_matrix.csv -t