1. RNAseq回帖到CDS序列

#!/bin/bash
#PBS -l nodes=1:ppn=30
#PBS -l walltime=999:00:00

cd /home/lx_sky6/yt/z99_call_gene
export PATH=/home/lx_sky6/software/miniconda3/bin/:$PATH

hisat2-build -p 30 DTB2.fa DTB2.fa

hisat2 -x DTB2.fa  -p 30 -1 /home/lx_sky6/yt/0110_DDM_YC_RNA/DDM/L1EGC170001--DDM_1_Y.R1.trim.fastq.gz -2 /home/lx_sky6/yt/0110_DDM_YC_RNA/DDM/L1EGC170001--DDM_1_Y.R2.trim.fastq.gz  --no-unal |/home/lx_sky6/software/miniconda3/envs/yt/bin/samtools sort -m 10G -@ 10  > DTB2.rna.bam

2. 2代数据回帖到基因组序列

#!/bin/bash
#PBS -l nodes=1:ppn=30
#PBS -l walltime=999:00:00

cd /home/lx_sky6/yt/z99_call_gene
bowtie2-build DTB1.genome.fa DTB1.genome.fa
bowtie2 -p 30 --local -x DTB1.genome.fa  -1 /data/0.user_data/lx_sky6/yt/DDM_survey/0109_diandimei_survry/Unknown_BB398-01R0001_good_1.fq.gz  -2 /data/0.user_data/lx_sky6/yt/DDM_survey/0109_diandimei_survry/Unknown_BB398-01R0001_good_2.fq.gz  -S DTB1.genome.sam
##排序
/home/lx_sky6/software/miniconda3/envs/yt/bin/samtools view -bS DTB1.genome.sam > DTB1.genome.bam
/home/lx_sky6/software/miniconda3/envs/yt/bin/samtools view -bF 4 DTB1.genome.bam > DTB1.genome_filter.bam 

将对应的cds/rna.bam和gene_genome.fa/gene_genome.bam拖入到genious里面查看