hisat2_mapping

when you want to mapping some file no blast,for example fq type file,you should download hisat2 software.
you should try below command
first and foremost,you should found the genome file,fa type file.
then you use:$hisat2-build -p 10 file.fa file<prefix> build database. #must be fa file to build the database
On lower version hisat-build,not the thread parameter,just use the line command $hisat-build .fa filename<prefix> done
then you copy you query seq file,for instance,fastq type file.
hisat2 -p 10 -x <database_genome prefix> -1 a.fastq -2 b.fastq -S test.sam &>mapping.log #　-S output file sam　type,and log　file
comment:the prefix not comprehend ".fa" like the string "Nosema_bombycis_CQ1.NosBomCQ1_v1.0.genome" not including the "Nosema_bombycis_CQ1.NosBomCQ1_v1.0.genome.fa"


comment:-p thread counts.
the mapping rate on the log file.
overall aligned rate:.....94.44%