Running and Verifying HISAT2

Use PuTTY to log in to the server as the root user.
Run the following command to go to the /path/to/CASE directory:
```
cd /path/to/CASE
```
Run the following command to set the environment variables for the HISAT executable file:
```
export PATH=/path/to/HISAT2/hisat2-2.1.0/:$PATH
```
Run the following command to decompress bdgp6.tar.gz, which is listed in Table 2:
```
cd /path/to/CASE
tar -xvf bdgp6.tar.gz
cd bdgp6
```
Run the following commands to modify the make_bdgp6.sh file:
1. Open make_bdgp6.sh.
```
vi make_bdgp6.sh
```
2. Press i to enter the insert mode and comment out the following line:
```
# ENSEMBL_BASE=ftp://xxxxxxxx
```
3. Press Esc, type :wq!, and press Enter to save the file and exit.
Use an SFTP tool to copy the Drosophila_melanogaster.BDGP6.dna.toplevel.fa.gz file to the /path/to/CASE/bdgp6 directory.

Run the following commands to decompress the files:

gzip -d Homo_sapiens.GRCh38.86.chr.gtf.gz
gzip -d R1.fq.gz
gzip -d R2.fq.gz

Run the following command to run the make_bdgp6.sh file:
```
./make_bdgp6.sh
```

Run the following commands to create the transcriptome.

extract_exons.py Homo_sapiens.GRCh38.86.chr.gtf > genome.exon
extract_splice_sites.py Homo_sapiens.GRCh38.86.chr.gtf > genome.ss

Run the following command to index the genome and transcriptome:

hisat2-build -p96 genome.fa --ss genome.ss --exon genome.exon genome_tran

Parent topic: HISAT2 2.1.0 Porting Guide (CentOS 7.6)