RNA-Seq technology has been gradually becoming a routine approach for 
characterizing the properties of transcriptome in terms of organisms, cell types 
and conditions and consequently a big burden has been put on the facet of data 
analysis, which calls for an easy-to-learn workflow to cope with the increased 
demands from a large number of laboratories across the world. We report a 
one-in-all solution called hppRNA, composed of four scenarios such as 
pre-mapping, core-workflow, post-mapping and sequence variation detection, 
written by a series of individual Perl and R scripts, counting on 
well-established and preinstalled software, irrespective of single-end or 
paired-end, unstranded or stranded sequencing method. It features six 
independent core-workflows comprising the state-of-the-art technology with 
dozens of popular cutting-edge tools such as Tophat-Cufflink-Cuffdiff, 
Subread-featureCounts-DESeq2, STAR-RSEM-EBSeq, Bowtie-eXpress-edgeR, 
kallisto-sleuth, HISAT-StringTie-Ballgown, and embeds itself in Snakemake, which 
is a modern pipeline management system. The core function of this pipeline is 
turning the raw fastq files into gene/isoform expression matrix and 
differentially expressed genes or isoforms as well as the identification of 
fusion genes, single nucleotide polymorphisms, long noncoding RNAs and circular 
RNAs. Last but not least, this pipeline is specifically designed for performing 
the systematic analysis on a huge set of samples in one go, ideally for the 
researchers who intend to deploy the pipeline on their local servers. The 
scripts as well as the user manual are freely available at 
https://sourceforge.net/projects/hpprna/.