Hi,

I used below script to run Hisat2 for multiple pair end read files to map on reference genome separately. I got the sam file but it did not generate the statistics of read mapping, is it still possible to get read mapping statistics from sam files?

#!/bin/bash
#SBATCH --job-name=mpi_job_test      # Job name
#SBATCH --mail-type=END,FAIL         # Mail events (NONE, BEGIN, END, FAIL, ALL)     
#SBATCH --ntasks=8                  # Number of MPI ranks
#SBATCH --cpus-per-task=1            # Number of cores per MPI rank 
#SBATCH --nodes=1                    # Number of nodes
#SBATCH --time=200:05:00              # Time limit hrs:min:sec

#SBATCH --partition=lowpri


#RUN_Hisat2

module add hisat2/2.1.0


hisat2 -x chrX_tran -1 Leaf_T1_F_R10_S1_L001_R1_paired.fq.gz -2 Leaf_T1_F_R10_S1_L001_R2_paired.fq.gz -S Leaf_T1_F_R10_S1_L001.sam

hisat2 -x chrX_tran -1 Leaf_T1_F_R2_S5_L001_R1_paired.fq.gz -2 Leaf_T1_F_R2_S5_L001_R2_paired.fq.gz -S Leaf_T1_F_R2_S5_L001.sam

hisat2 -x chrX_tran -1 Leaf_T1_F_R3_S4_L001_R1_paired.fq.gz -2 Leaf_T1_F_R3_S4_L001_R2_paired.fq.gz -S Leaf_T1_F_R3_S4_L001.sam

Many thanks nabiyogesh