轉(zhuǎn)錄分析流程
#!/bin/bash
set -e
set -o
for file1 in *_1.clean.fq.gz
do
#? echo $file1
file2=$(echo ${file1} | sed 's/_1.clean.fq.gz/_2.clean.fq.gz/')
name=$(echo ${file1} | sed 's/_1.clean.fq.gz//')
#!/bin/bash
#$ -cwd
#$ -S /bin/bash
#$ -j y
#$ -pe mpi 24
#$ -q all.q
echo "/PATH/to/hisat2-2.1.0/hisat2 -p 24 --dta-cufflinks -x? PATH/to/reference_index/*** -1 PATH/to/$file1 -2 PATH/to/$file2 -S /PATH/to/cufflinks/sam_file/$file1.sam
PATH/to/samtools sort -@ 10 -o PATH/to/cufflinks/sam_file/$file1.bam PATH/to/cufflinks/sam_file/$file1.sam
PATH/to/cufflinks-2.2.1.Linux_x86_64/cufflinks -p 24 -G PATH/to/***.gff3 -o /PATH/to/cufflinks/sam_file/$file1.assemble PATH/to/cufflinks/sam_file/$file1.bam" > $name.sh
done
