Subread

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 cluster
  • SC 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 20 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

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