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!
Hello lakshmi9c!
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I thought this was a better question than the original because it (i) mentions Ballgown in the title, (ii) links to the relevant protocol that is being followed and (iii) doesn't tag a whole lot of other packages. Tagging the ballgown package would have been even better. I would have preferred to close the earlier question in favour of this one.
This is different to the last post, I am enquiring about the different normalisation protocols available using R for differential gene expression. Kindly reopen this thread.