Hi I'm working on RNA-Seq analysis to get differentially expressed genes between two sample conditions. I'm following the new Tuxedo pipeline- HISAT STRINGTIE BALLGOWN. My concern is about using ballgown package for differential expression analysis of my RNA-Seq data. I have tried looking up manuals/ protocol for running Ballgown on R. But unfortunately, I can't find a standard protocol. I have run all commands correctly as per paper- https://www.nature.com/articles/nprot.2016.095. • But I don't understand the need to remove low variance transcripts. Isn't low variance transcripts and low gene abundance entirely different? • How do I get gene name and gene id without stattest() function on R using ballgown? • How is normalisation done for Ballgown?
I'm unable to proceed after getting the list of gene names and unsure of what the next step is. How should I do normalisation for Ballgown? I'm stuck at this step and would much appreciate any help on how do I proceed in order to get DE genes. Thanks in advance!