Entering edit mode
4.4 years ago
Bioinfonext
▴
460
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
Please use the search function:
How To Get Mapping Statistics On Bam File
Rna-Seq Read Mapping Stats/Metrics