Difference between revisions of "Applications/STAR"

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Basic STAR workflow consists of 2 steps:
 
Basic STAR workflow consists of 2 steps:
  
* Generating genome indexes files. 2nd (mapping) step. The genome indexes are saved to disk and need only be generated once for each genome/annotation combination.  
+
* 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, and writes several output files, such as alignments (SAM/BAM), mapping summary statistics, splice junctions, nmapped reads, signal (wiggle) tracks etc.  
+
* 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.  
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===Command Description===
 
===Command Description===
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===Module===
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===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
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[username@login01 ~]$ STAR --option1-name option1-value(s)--option2-name option2-value(s)
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[username@login01 ~]$ interactive
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salloc: Granted job allocation 3619731
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Job ID 3619731 connecting to c081, please wait...
 +
c081.vc-main
 +
 
 +
[username@c081 ~]$ module add STAR/2.6.1
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[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
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#SBATCH -J jobname                # Job name, you can change it to whatever you want
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#SBATCH -n 4                      # Number of cores
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#SBATCH -o %N.%j.out              # Standard output will be written here
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#SBATCH -e %N.%j.err              # Standard error will be written here
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#SBATCH -p compute                # Slurm partition, where you want the job to be queued
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#SBATCH -t=20:00:00              # Run for 20 hours
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#SBATCH --mail-user=your email    # Mail to email address when finished
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module purge
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module add STAR/2.6.1
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STAR --option1-name option1-value(s)--option2-name option2-value(s)
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 +
</pre>
  
 
==Further Information==
 
==Further Information==
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* [https://github.com/alexdobin/STAR https://github.com/alexdobin/STAR]
 
* [https://github.com/alexdobin/STAR https://github.com/alexdobin/STAR]
  
==Navigation==
+
{{Modulepagenav}}
 
 
* [[Main_Page|Home]]
 
* [[Applications|Application support]] *
 
* [[General|General]]
 
* [[Programming|Programming support]]
 

Latest revision as of 11:36, 17 November 2022

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)

Further Information





Modules | Main Page | Further Topics