We can align reads to the genome using a software such as hisat2.
Download the appropriate index from the hisat2 website to our
annotation directory, and then run tar -xvf on the file that
you download (it will create a directory). Note that grch38 (human)
is already downloaded to our lab space (as shown below).
A simple bash script for running hisat2 on some paired-end reads is then:
#!/bin/bash
#
#SBATCH --job-name=align
#SBATCH --time=120
#SBATCH --mem=10000
#SBATCH -n 12
#SBATCH -N 1
module load hisat2
module load samtools
hisat2 -p 12 -x /proj/milovelab/anno/grch38/genome \
-1 reads_01.fastq.gz \
-2 reads_02.fastq.gz \
-S file.sam
samtools view -bS file.sam > file.bam
samtools sort file.bam -o file.sorted.bam
samtools index file.sorted.bam
Note: if you are generating simulated reads with Polyester,
you will need to add -f for FASTA input.