Running and Verifying STAR

Procedure

Use PuTTY to log in to the server as the root user.
Run the following command to switch to the directory where the test cases are stored:
```
cd /path/to/CASE
```

Run the following commands to decompress the test case packages:

gzip -d Homo_sapiens.GRCh38.dna.chromosome.2.fa.gz
gzip -d Homo_sapiens.GRCh38.86.chr.gtf.gz

Run the following commands to create a genome index:

mkdir chr1_hg38_index
{ time STAR --runThreadN 96 --genomeSAindexNbases 12 --runMode genomeGenerate --genomeDir chr1_hg38_index --genomeFastaFiles Homo_sapiens.GRCh38.dna.chromosome.2.fa --sjdbGTFfile Homo_sapiens.GRCh38.86.chr.gtf --sjdbOverhang 99 ; } 2>&1 |tee genome-index.log

Run the following command to compare genomes:

{ time STAR --runMode alignReads --outSAMtype BAM Unsorted --readFilesCommand zcat --genomeDir chr1_hg38_index/ --outFileNamePrefix Homo_sapiens.GRCh38 --readFilesIn TG_r1.fastq.gz TG_r2.fastq.gz ; } 2>&1 |tee Mapping.log

After the genome comparison is complete, the following files and directories are generated:
- Homo_sapiens.GRCh38Aligned.out.bam
- Homo_sapiens.GRCh38Log.final.out
- Homo_sapiens.GRCh38Log.out
- Homo_sapiens.GRCh38Log.progress.out
- Homo_sapiens.GRCh38SJ.out.tab
- Homo_sapiens.GRCh38_STARtmp
When the genome index is created and genome comparison is performed, the software does not automatically generate logs about the running time or performance. You need to run the time command to redirect the entire running time to the log file.
View the real value (x minutes y seconds) in the last time command output in the log. A smaller value indicates higher performance.

Information similar to the following is displayed.
```
[root@XA320V2-19 CASE]# cat Mapping.log
Jan 16 20:42:41 ..... started STAR run
Jan 16 20:42:41 ..... loading genome
Jan 16 20:42:42 ..... started mapping
Jan 16 20:42:53 ..... finished mapping
Jan 16 20:42:53 ..... finished successfully
real    0m11.581s
user    0m10.703s
sys     0m0.579s
```

Parent topic: STAR 2.7.1a Porting Guide (CentOS 7.6)