Txseq provides a suite of modular workflows for the QC and analysis of bulk RNA-sequencing data on high-performance compute clusters. These include pipelines for sanitising Ensembl annotations for RNA-seq analysis, building transcriptome indexes and performing quality control with Fastqc and Picard tools. Pipelines for traditional alignment-based mapping with Hisat2 and quantitation with featureCounts are provided along with a more-modern pseudo-alignment workflow that incorporates Salmon and tximeta. Template reports for sequence quality, post-mapping qc analysis, exploratory data analysis and differential gene expression are provided as Rmarkdown notebooks.
For further information please see the docs: https://txseq.readthedocs.io