Difference between revisions of "Applications/Crop"
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==Usage== | ==Usage== | ||
| − | CROP, which stands for "Clustering 16s rRNA for OTU Prediction", is a software developed in Ting Chen's Lab at University of Southern California in 2011 by Haoxiao Lin, Rui Jiang and Ting Chen. | + | CROP, which stands for "Clustering 16s rRNA for OTU Prediction", is a software developed in Ting Chen's Lab at the University of Southern California in 2011 by Haoxiao Lin, Rui Jiang and Ting Chen. |
CROP is an unsupervised nucleic acid sequence clustering algorithm. The algorithm sees the OTUs as a Gaussian mixture and models the clustering process using Birth-death MCMC. This approach makes the OTU prediction more accurate. | CROP is an unsupervised nucleic acid sequence clustering algorithm. The algorithm sees the OTUs as a Gaussian mixture and models the clustering process using Birth-death MCMC. This approach makes the OTU prediction more accurate. | ||
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To know more about the theoretical basis of CROP, please refer to the following paper: Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering, Bioinformatics (2011) | To know more about the theoretical basis of CROP, please refer to the following paper: Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering, Bioinformatics (2011) | ||
| − | === | + | ===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 crop/1.33/gcc-6.3.0 | + | [username@login01 ~]$ interactive |
| − | [username@ | + | salloc: Granted job allocation 3619731 |
| + | Job ID 3619731 connecting to c081, please wait... | ||
| + | c081.vc-main | ||
| + | |||
| + | [username@c081 ~]$ module add crop/1.33/gcc-6.3.0 | ||
| + | [username@c081 ~]$ CROPLinux –i MyInput.fasta | ||
</pre> | </pre> | ||
| − | + | ===Batch Script=== | |
| + | |||
| + | <pre style="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 crop/1.33/gcc-6.3.0 | ||
| + | CROPLinux –i MyInput.fasta | ||
| + | |||
| + | </pre> | ||
| + | See https://github.com/tingchenlab/CROP/blob/master/CROP%20User's%20Guide%20v1.33.pdf for further details on the options used. | ||
| − | == | + | ==Next Steps== |
* [https://github.com/tingchenlab/CROP https://github.com/tingchenlab/CROP] | * [https://github.com/tingchenlab/CROP https://github.com/tingchenlab/CROP] | ||
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Latest revision as of 14:25, 17 November 2022
Application Details
- Description:
- Version: 1.33 (compiled with gcc-6.3.0)
- Module: crop/1.33/gcc-6.3.0
- Licence: GNU
Usage
CROP, which stands for "Clustering 16s rRNA for OTU Prediction", is a software developed in Ting Chen's Lab at the University of Southern California in 2011 by Haoxiao Lin, Rui Jiang and Ting Chen.
CROP is an unsupervised nucleic acid sequence clustering algorithm. The algorithm sees the OTUs as a Gaussian mixture and models the clustering process using Birth-death MCMC. This approach makes the OTU prediction more accurate.
To know more about the theoretical basis of CROP, please refer to the following paper: Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering, Bioinformatics (2011)
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 crop/1.33/gcc-6.3.0 [username@c081 ~]$ CROPLinux –i MyInput.fasta
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 crop/1.33/gcc-6.3.0 CROPLinux –i MyInput.fasta
See https://github.com/tingchenlab/CROP/blob/master/CROP%20User's%20Guide%20v1.33.pdf for further details on the options used.