In regards to RNAseq analysis:
I’m in the process of analysing RNA-seq data and I initially followed the HISAT2-StringTie-Ballgown pipeline, however, the most up to date version of ballgown does not recognize my StringTie files for some reason? It only recognizes tables from StringTiemerge, even tho the other StringTie outputs appear to be in the same format (tabular). I attempted an older version of Ballgown, which does recognize the StringTie files, however, it fails immediately after launching. I am now attempting to run Cuffquant to subsequently run Cuffdiff, thus trying a different pipeline, but I know the tools are deprecated and they are running very slowly.
I was hoping someone might have some tips regarding Ballgown, or could clarify if Cuffquant/Cuffdiff are still okay to use?