[](https://travis-ci.org/datasnakes/htseq-count-cluster)
htseq-count-cluster
A cli wrapper for running [htseq](https://github.com/simon-anders/htseq)'s `htseq-count` on a cluster.
View [documentation](https://tinyurl.com/yb7kz7zz).
Install
`pip install HTSeqCountCluster`
Features
- For use with large datasets (we've previously used a dataset of 120 different human samples)
- For use with SGE/SGI cluster systems
- Submits multiple jobs
- Command line interface/script
- Merges counts files into one counts table/csv file
- Uses `accepted_hits.bam` file output of `tophat`
Examples
Run htseq-count-cluster
After generating bam output files from tophat, instead of using HTSeq's htseq count, you
can use our `htseq-count-cluster` script. This script is intended for use with
clusters that are using pbs (qsub) for job monitoring.
bash
htseq-count-cluster -p path/to/samples/ -f samples.csv -g genes.gtf -o path/to/cluster-output/
This script uses logzero so there will be color coded logging information to your shell.
A common linux practice is to use `screen` to create a new shell and run a program
so that if it does produce output to the stdout/shell, the user can exit that particular
shell without the program ending and utilize another shell.
Help message output
usage: htseq_count_cluster.py [-h] -p INPATH -f INFILE -g GTF -o OUTPATH
[-e EMAIL]
This is a command line wrapper around htseq-count.
optional arguments:
-h, --help show this help message and exit
-p INPATH, --inpath INPATH
Path of your samples/sample folders.
-f INFILE, --infile INFILE
Name or path to your input csv file.
-g GTF, --gtf GTF Name or path to your gtf/gff file.
-o OUTPATH, --outpath OUTPATH
Directory of your output counts file. The counts file
will be named.
-e EMAIL, --email EMAIL
Email address to send script completion to.
*Ensure that htseq-count is in your path.
Merge output counts files
In order to prep your data for `DESeq2`, `limma` or `edgeR`, it's best to have 1 merged
counts file instead of multiple files produced from the `htseq-count-cluster` script. We offer this
as a standalone script as it may be useful to keep those files separate.
bash
merge-counts -d path/to/cluster-output/
Help message for mergecounts.py
usage: mergecounts.py [-h] -d DIRECTORY
Merge multiple counts tables into 1 counts .csv file.
Your output file will be named: merged_counts_table.csv
optional arguments:
-h, --help show this help message and exit
-d DIRECTORY, --directory DIRECTORY
Path to folder of counts files.
ToDo
- [ ] Monitor jobs.
- [ ] Enhance wrapper input for other use cases.
- [ ] Add example data.
Maintainers
Shaurita Hutchins | [sdhutchins](https://github.com/sdhutchins) | [✉](mailto:sdhutchinsoutlook.com)
Rob Gilmore | [grabear](https://github.com/grabear) | [✉](mailto:robgilmore127gmail.com)
Help
Please feel free to [open an issue](https://github.com/datasnakes/htseq-count-cluster/issues/new) if you have a question/feedback/problem
or [submit a pull request](https://github.com/datasnakes/htseq-count-cluster/compare) to add a feature/refactor/etc. to this project.