Creating a Bowtie Index

Use PuTTY to log in to the server as the root user.
Run the following command to switch to the CHROMFA directory:
```
cd /path/to/CHROMFA
```
Run the following command to decompress the chromFa installation package:
```
tar -xzvf chromFa.tar.gz
```
Run the following command to perform the redirection:
```
cat *.fa > man.fa
```
Run the following command to create an index:
```
bowtie-build --threads 128 man.fa man_index
```
Run the following commands to create a man_hg19 directory and save the generated man_index*.ebwt file to this directory:
```
mkdir man_hg19
mv  *.ebwt  man_hg19
```

Parent topic: Compiling and Installing Bowtie