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Overview
HTSeq: Analysing high-throughput sequencing data with Python.
Using
Use the module name htseq to discover versions available and to load the application.
Older versions can be found using py-htseq
Example
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[]$ module load htseq/0.12.4
[]$ htseq-count --help
[]$ htseq-count-barcodes --help
[]$ htseq-qa --help |
Parallelization:
Note that the htseq-count command allow the use of multiple cores:
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[]$ htseq-count --help
...
-n NPROCESSES, --nprocesses NPROCESSES Number of parallel CPU processes to use (default: 1).
... |
Within you slurm sbatch script use the --cpus-per-task option, and then set the htseq-count -n value to the same number.
To use 16 cores on a single node, a basic template would look like the following:
...
Multicore
Some of the htseq related commands can run across multiple cores. View their usage details to find out which, for example view htseq-count --help to view its -n / --nprocesses option.