Day: May 23, 2024

1. Download -version HISAST2 2.2.1 OSX_X86_64 : https://daehwankimlab.github.io/hisat2/download/#version-hisat2-221
2. Put everything proper location: eg) /Users/___/___/hisat2-2.2.1
3. Add Path into .zshrc: export PATH=$PATH:/Users/___/___/hisast2-2.2.1
4. Download reference seq: eg) wget  https://genome-idx.s3.amazonaws.com/hisat/mm10_genome.tar.gz
5. Need unzip: eg) tar -xvf mm10_genome.tar.gz
6. Run alignment: eg) hisat2 -q –rna-strandness R -x hISAT2/mm10/genome -U data/SRR2936865_trimmed.fastq.gz | samtools sort -o HISAT2/SRR2936865.bam

If you need some more help:

Installation: