Difference between revisions of "Subread"
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== Description == | == Description == | ||
!!! Documentation under construction !!! | |||
''From the Subread Home Page:'' '''Subread''' The Subread package comprises a suite of software programs for processing next-gen sequencing read data. Note that this package includes Subread, featureCount, and Subjunc. | ''From the Subread Home Page:'' '''Subread''' The Subread package comprises a suite of software programs for processing next-gen sequencing read data. Note that this package includes Subread, featureCount, and Subjunc. | ||
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=== Batch Job submission === | === Batch Job submission === | ||
To run batch jobs on the CIRCE/SC cluster, users will need to submit their jobs to the scheduling environment if their jobs take more than | To run batch jobs on the CIRCE/SC cluster, users will need to submit their jobs to the scheduling environment if their jobs take more than 30 minutes to run on a standard PC. | ||
Note: for featureCounts, there are prebuilt annotation indexes in /apps/subread/1.6.0/annotation for the two most recent human and mouse genome builds (hg19 and hg38 for human, mm9 and mm10 for mouse, respectively). | Note: for featureCounts, there are prebuilt annotation indexes in /apps/subread/1.6.0/annotation for the two most recent human and mouse genome builds (hg19 and hg38 for human, mm9 and mm10 for mouse, respectively). |
Latest revision as of 15:37, 13 March 2023
Description
!!! Documentation under construction !!!
From the Subread Home Page: Subread The Subread package comprises a suite of software programs for processing next-gen sequencing read data. Note that this package includes Subread, featureCount, and Subjunc.
Separately, the same features are available as an R package, Rsubread. This can be installed via Bioconductor:
#within R ## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("Rsubread") browseVignettes("Rsubread") #to see R steps similar to below analysis
Version
- 1.6.0
Authorized Users
- CIRCE account holders
- SC account holders
Platforms
CIRCE
clusterRRA
clusterSC
cluster
Modules
- apps/subread/1.6.0
Running Subread on CIRCE/SC
The Subread user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.
- Note on CIRCE: Make sure to run your jobs from your $WORK directory!
- Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.
Batch Job submission
To run batch jobs on the CIRCE/SC cluster, users will need to submit their jobs to the scheduling environment if their jobs take more than 30 minutes to run on a standard PC.
Note: for featureCounts, there are prebuilt annotation indexes in /apps/subread/1.6.0/annotation for the two most recent human and mouse genome builds (hg19 and hg38 for human, mm9 and mm10 for mouse, respectively).
Notable flags:
-T N , will set the number of compute cores to use, where N is the number of cores
-t 0/1 , specify whether data is DNA or RNA-seq in subread-align
For more information, please see the documentation at http://subread.sourceforge.net/ .
If, for example, you wish to use subread and featureCount, you would set up a submit script to use featureCounts like this:
#!/bin/bash #SBATCH --job-name=test_featureCount #SBATCH --time=04:00:00 #SBATCH -N 1 #SBATCH --ntasks-per-node=4 #SBATCH --mem-per-cpu=2096 #SBATCH -o output.%j.%N.txt #SBATCH -e error.%j.%N.txt #### SLURM single node sub test #### to run for 4 hours #### using 4 processing cores and 8GB of memory # Unload all modules, then load the subread module: module purge module load apps/subread/1.6.0 #always run in WORK when running batch jobs cd $HOME/featureCounts_ex/ cp hg38.fa $WORK cp SRR000001.fastq $WORK cd $WORK #computation steps #build genome index subread-buildindex -F -o hg38.ind -M8000 hg38.fa #assemble reads subread-align -i hg38.ind -t 1 -T 4 -r SRR000001.fastq -o subread_results.bam #count overlap of reads to annotation featureCounts -a /apps/subread/1.6.0/annotation/hg38_RefSeq_exon.txt -T 4 -F SAF -o counts.txt subread_results.bam #cleanup cp counts.txt $HOME/featureCounts_ex
Next, you can change to your job’s directory, and run the sbatch command to submit the job:
[user@login0 ~]$ cd my/jobdir [user@login0 jobdir]$ sbatch ./test_subread.sh
- You can view the status of your job with the “squeue -u <username>” command
Documentation
Home Page, User Guides, and Manuals
- Subread Home Page:
- Subread User Guide:
Benchmarks, Known Tests, Examples, Tutorials, and Other Resources
- Subread Examples
- /apps/subread/subread/1.6.0/examples
More Job Information
See the following for more detailed job submission information:
Reporting Bugs
Report bugs with Subread to the IT Help Desk: rc-help@usf.edu