Difference between revisions of "Applications/Bowtie2"
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<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
| − | [username@login01 ~]$ module load bowtie2/gcc/2.2.9 | + | [username@login01 ~]$ module add bowtie2/gcc/2.2.9 |
| + | |||
| + | </pre> | ||
| + | |||
| + | ===Batch Job=== | ||
| + | <!-- edited from https://wiki.rc.usf.edu/index.php/Bowtie2#Batch_Job_submission --> | ||
| + | <pre> | ||
| + | #!/bin/bash | ||
| + | #SBATCH -J test_bowtie2 | ||
| + | #SBATCH --time=04:00:00 | ||
| + | #SBATCH -n 4 | ||
| + | #SBATCH --mem=8G | ||
| + | #SBATCH -o output.%j.%N.out | ||
| + | #SBATCH -e error.%j.%N.err | ||
| + | |||
| + | # Unload all modules, then load the bowtie2 module: | ||
| + | module purge | ||
| + | module load bowtie2/gcc/2.2.9 | ||
| + | |||
| + | |||
| + | #always run in WORK when running batch jobs | ||
| + | mkdir $WORK/bowtie | ||
| + | cp $HOME/featureCounts_ex/*fa $WORK/bowtie | ||
| + | cp $HOME/featureCounts_ex/*fa* $WORK/bowtie | ||
| + | cp $HOME/trim_ex/SRR6202537_1.fastq $WORK/bowtie | ||
| + | cp $HOME/trim_ex/SRR6202537_2.fastq $WORK/bowtie | ||
| + | cd $WORK/bowtie | ||
| + | |||
| + | |||
| + | #computation steps | ||
| + | |||
| + | bowtie2-build --threads 4 hg38.fa hg38 | ||
| + | bowtie2 -p 4 -x hg38 -1 SRR6202537_1.fastq -2 SRR6202537_2.fastq -S SRR6202537.sam --no-unal | ||
| + | |||
| + | |||
| + | cp *.sam $HOME/bowtie_ex | ||
</pre> | </pre> | ||
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* [http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml] | * [http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml] | ||
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Latest revision as of 16:46, 16 November 2022
Application Details
- Description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
- Version: 2.2.9 (compiled with gcc)
- Modules: bowtie2/gcc/2.2.9
- Licence: Open source (Github)
Usage Examples
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
It provides the following tools:
- bowtie2
- bowtie2-align-l
- bowtie2-align-s
- bowtie2-build
- bowtie2-build-l
- bowtie2-build-s
- bowtie2-inspect
- bowtie2-inspect-l
- bowtie2-inspect-s
With linkages to the following modules too:
[username@login01 ~]$ module add bowtie2/gcc/2.2.9
Batch Job
#!/bin/bash #SBATCH -J test_bowtie2 #SBATCH --time=04:00:00 #SBATCH -n 4 #SBATCH --mem=8G #SBATCH -o output.%j.%N.out #SBATCH -e error.%j.%N.err # Unload all modules, then load the bowtie2 module: module purge module load bowtie2/gcc/2.2.9 #always run in WORK when running batch jobs mkdir $WORK/bowtie cp $HOME/featureCounts_ex/*fa $WORK/bowtie cp $HOME/featureCounts_ex/*fa* $WORK/bowtie cp $HOME/trim_ex/SRR6202537_1.fastq $WORK/bowtie cp $HOME/trim_ex/SRR6202537_2.fastq $WORK/bowtie cd $WORK/bowtie #computation steps bowtie2-build --threads 4 hg38.fa hg38 bowtie2 -p 4 -x hg38 -1 SRR6202537_1.fastq -2 SRR6202537_2.fastq -S SRR6202537.sam --no-unal cp *.sam $HOME/bowtie_ex