文件过滤_hisat2比对小不同：fastp过滤后和trim_galore过滤后文件

trim_galore过滤后的文件名：

SRR10428360_1_val_1.fq.gz

SRR10428360_2_val_2.fq.gz

index=/home/data/vip30/database/genome/Ensembl/Homo_sapiens/Homo_sapiens.GRCh38_release101.genomeinputdir=/home/data/vip30/data/rnaseq/GSE140202/cleandata/trim_galoreoutdir=/home/data/vip30/data/rnaseq/GSE140202/mapping/Hisacat /home/data/vip30/data/rnaseq/GSE140202/rawdata/SraAccList.txt | while read iddo  echo "hisat2 -p 16 -x ${index} -1 ${inputdir}/${id}_1_val_1.fq.gz -2 ${inputdir}/${id}_2_val_2.fq.gz 2>${id}.log  | samtools sort -@ 1 -o ${outdir}/${id}.Hisat_aln.sorted.bam -  && samtools index ${outdir}/${id}.Hisat_aln.sorted.bam ${outdir}/${id}.Hisat_aln.sorted.bam.bai"done >Hisat.shnohup sh Hisat.sh >Hisat.log &

index：索引

in