A cli wrapper for running htseq's
htseq-count on a cluster.
pip install HTSeqCountCluster
- 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
accepted_hits.bamfile output of
After generating bam output files from tophat, instead of using HTSeq's
can use our
htseq-count-cluster script. This script is intended for use with
clusters that are using pbs (qsub) for job monitoring.
htseq-count command is
htseq-count -f bam -s no file.bam file.gtf -o htseq.out.
This command does not take into account any strandedness (
-s no) for the input bamfiles (
-f bam) and uses the default
union mode. For the default mode
union, only the aligned read determines how the read pair is counted.
htseq-count-cluster -p path/to/bam-files/ -f samples.csv -g genes.gtf -o path/to/cluster-output/
||This is the path of your .bam files. Presently, this script looks for a folder that is the sample name and searches for an accepted_hits.bam file (tophat output).||Yes|
||You should have a csv file list of your samples or folder names (no header).||Yes|
||This should be the path to your genes.gtf file.||Yes|
||This should be an existing directory for your output counts files.||Yes|
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 for
usage: htseq-count-cluster [-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
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.
merge-counts -d path/to/cluster-output/
Help message for
usage: merge-counts [-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.
- Monitor jobs.
- Enhance wrapper input for other use cases.
- Add example data.
Simon Anders, Paul Theodor Pyl, Wolfgang Huber; HTSeq—a Python framework to work with high-throughput sequencing data, Bioinformatics, Volume 31, Issue 2, 15 January 2015, Pages 166–169, https://doi.org/10.1093/bioinformatics/btu638