This Snakemake pipeline automates a RNAseq workflow utilizing bash command line tools, fastqc trimmomatic, hisat2 and htseq-count. The input of this pipeline is a fastq.gz file and produces a count matrix file, for further differential expression analysis.
- conda
- snakemake
- fastqc
- trimmomatic-PE
- hisat2
- htseq-count
Contributions to the package are more than welcome. If you want to contribute to this package, you should follow the same conventions as the rest of the functions. Please do get in touch (preferable opening a github issue) to discuss any suggestions.
Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.