Difference between revisions of "Applications/STAR"
From HPC
m (→Navigation) |
m (→Usage) |
||
| (One intermediate revision by the same user not shown) | |||
| Line 11: | Line 11: | ||
Basic STAR workflow consists of 2 steps: | Basic STAR workflow consists of 2 steps: | ||
| − | * Generating genome | + | * Generating genome index files. 2nd (mapping) step. The genome indexes are saved to disk and need only be generated once for each genome/annotation combination. |
| − | * Mapping reads to the genome. In this step user supplies the genome files generated in the 1st step, as well as the RNA-seq reads (sequences) in the form of FASTA or FASTQ files. STAR maps the reads to the genome | + | * Mapping reads to the genome. In this step, the user supplies the genome files generated in the 1st step, as well as the RNA-seq reads (sequences) in the form of FASTA or FASTQ files. STAR maps the reads to the genome and writes several output files, such as alignments (SAM/BAM), mapping summary statistics, splice junctions, nmapped reads, signal (wiggle) tracks etc. |
| + | |||
===Command Description=== | ===Command Description=== | ||
| Line 23: | Line 24: | ||
| − | === | + | ===Interactive Session=== |
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | <pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
| − | [username@login01 ~]$ module add STAR/2.6.1 | + | |
| − | [username@ | + | [username@login01 ~]$ interactive |
| + | salloc: Granted job allocation 3619731 | ||
| + | Job ID 3619731 connecting to c081, please wait... | ||
| + | c081.vc-main | ||
| + | |||
| + | [username@c081 ~]$ module add STAR/2.6.1 | ||
| + | [username@c081 ~]$ STAR --option1-name option1-value(s)--option2-name option2-value(s) | ||
</pre> | </pre> | ||
| + | ===Batch Script=== | ||
| + | |||
| + | <pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
| + | |||
| + | #!/bin/bash | ||
| + | #SBATCH -J jobname # Job name, you can change it to whatever you want | ||
| + | #SBATCH -n 4 # Number of cores | ||
| + | #SBATCH -o %N.%j.out # Standard output will be written here | ||
| + | #SBATCH -e %N.%j.err # Standard error will be written here | ||
| + | #SBATCH -p compute # Slurm partition, where you want the job to be queued | ||
| + | #SBATCH -t=20:00:00 # Run for 20 hours | ||
| + | #SBATCH --mail-user=your email # Mail to email address when finished | ||
| + | |||
| + | module purge | ||
| + | module add STAR/2.6.1 | ||
| + | STAR --option1-name option1-value(s)--option2-name option2-value(s) | ||
| + | </pre> | ||
==Further Information== | ==Further Information== | ||
Latest revision as of 11:36, 17 November 2022
Contents
Application Details
- Description: RNA-seq aligner
- Version: 2016-10-27, 2.6.1
- Module: STAR/2016-10-27 and STAR/2.6.1
- Licence: Copyrighted by the Regents of the University of Minnesota. It can be freely used for educational and research purposes.
Usage
Basic STAR workflow consists of 2 steps:
- Generating genome index files. 2nd (mapping) step. The genome indexes are saved to disk and need only be generated once for each genome/annotation combination.
- Mapping reads to the genome. In this step, the user supplies the genome files generated in the 1st step, as well as the RNA-seq reads (sequences) in the form of FASTA or FASTQ files. STAR maps the reads to the genome and writes several output files, such as alignments (SAM/BAM), mapping summary statistics, splice junctions, nmapped reads, signal (wiggle) tracks etc.
Command Description
STAR command line has the following format:
STAR --option1-name option1-value(s)--option2-name option2-value(s) ...
If an option can accept multiple values, they are separated by spaces, and in a few cases - by commas.
Interactive Session
[username@login01 ~]$ interactive salloc: Granted job allocation 3619731 Job ID 3619731 connecting to c081, please wait... c081.vc-main [username@c081 ~]$ module add STAR/2.6.1 [username@c081 ~]$ STAR --option1-name option1-value(s)--option2-name option2-value(s)
Batch Script
#!/bin/bash #SBATCH -J jobname # Job name, you can change it to whatever you want #SBATCH -n 4 # Number of cores #SBATCH -o %N.%j.out # Standard output will be written here #SBATCH -e %N.%j.err # Standard error will be written here #SBATCH -p compute # Slurm partition, where you want the job to be queued #SBATCH -t=20:00:00 # Run for 20 hours #SBATCH --mail-user=your email # Mail to email address when finished module purge module add STAR/2.6.1 STAR --option1-name option1-value(s)--option2-name option2-value(s)