I am trying to follow the RNA-seq protocol described in (this excellent paper):
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks (2012) http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html
This was published three/four years ago, so not that much in terms of scientific timeline - but I noticed the tools described in the pipeline have not been updated in a while or have been replaced by other software. More specifically:
- TopHat has entered a low maintenance, low support stage as it is now largely superseded by HISAT2 (ref: https://ccb.jhu.edu/software/tophat/index.shtml)
- The github (https://github.com/cole-trapnell-lab/cufflinks) repo for cufflinks hasn't been recently updated (in about a year)
- Samtools is now at version 1.3.1, but this doesn't work with the current version of cufflinks (0.1.19 works though)
I know there are other software components which can replace some of the above (e.g. Star aligner instead of bowtie/tophat). I understand that the standard answer is "depends on what you want to do" (differential gene expression and variant analysis in my case - from human samples).
My question to the community is - what is a modern bioinformatics software pipeline to carry out RNAseq analysis?
Thanks for your suggestions or comments you may have,