generate_bam_file_and_unmapping_fastq

you need some bam file,unmapping clean data and mapping clean data,below command must be given.
samtools and bedtools must be installed.
so,let's begin.
First and foremost,we should download the project genome.(NCBI,NR for example).
$samtools faidx genome.fasta   
use hisat2 generate sam file.
$mkdir /home/hui/Result/L01 && cd /share/nas1/honghh/BBactrocera_dorsalis_Hendel/Result/L01 
&& /home/software/hisat/2.0.4/hisat2 --dta -p 6 --rna-strandness RF -x 
/home/hui/database/Bactrocera_dorsalis.ASM78921v2.genome   #this is prefix
-1 /home/data/Bactrocera_1.fq -2 /home/data/Bactrocera_2.fq -S 
/home/hui/Result/L01/L01.HISAT_aln.sam 
>/home/hui/Result/L01/L01.log
comment:use sh
samtobam
/home/hui/software/Bactrocera_dorsalis_Hendel/samtools-1.9/samtools view -bS 
/home/hui/Bactrocera_dorsalis_Hendel/Result/L12/L12.HISAT_aln.sam 
> /home/hui/Bactrocera_dorsalis_Hendel/Result/L12/L12.HISAT_aln.bam
sortbam
/samtools/0.1.18/samtools sort /Bactrocera_dorsalis_Hendel/Result/L05/L05.HISAT_aln.bam /Bactrocera_dorsalis_Hendel/Result/L05/L05.HISAT_aln_sort
filter bam_pair unmapping genome:
samtools view -bf 12 /Bactrocera_dorsalis_Hendel/Result/L01/L01.HISAT_aln_sort.bam >  #12 represent pair unmapping genome
/Bactrocera_dorsalis_Hendel/Result/L01/L01.HISAT_aln_sort_filter_12.bam
bamintofastq:
bedtools bamtofastq -i L01.HISAT_aln_sort_filter_12.bam -fq L01.HISAT_aln_1.fastq -fq2 L01.HISAT_aln_2.fastq  #pair mate,if no， -fq will be fine.