index=/media/pc/disk1/sun/refdata/ensembl_GRCm38/02_hisat2_all_index/genome_snp_tran

for i in `cat /media/pc/disk3/sun/20181112-RNAseq-QMJ-shf/list.txt`; do echo "$i" trimming.....; trimmomatic PE -phred33 -threads 20 "$i"1.fastq.gz "$i"2.fastq.gz "$i"1.fastq.clean.gz "$i"1.fastq.unpaired.gz "$i"2.fastq.clean.gz "$i"2.fastq.unpaired.gz ILLUMINACLIP:/home/pc/miniconda3/pkgs/trimmomatic-0.38-1/share/trimmomatic-0.38-1/adapters/TruSeq3-PE.fa:2:30:10:8:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 AVGQUAL:20 MINLEN:36; done && for i in `cat /media/pc/disk3/sun/20181112-RNAseq-QMJ-shf/list.txt`; do echo "$i" mapping.....; hisat2 -p 15 -x $index -5 3 -1 "$i"1.fastq.clean.gz -2 "$i"2.fastq.clean.gz -S "$i".sam --add-chrname --summary-file "$i".hisat2.txt; done && for i in `cat /media/pc/disk3/sun/20181112-RNAseq-QMJ-shf/list.txt`; do echo $i samtools.....; samtools view -@ 20 -m 2G -bS "$i".sam -o "$i".bam; done