Differential gene expression using Ballgown
0
0
Entering edit mode
lakshmi9c • 0
@lakshmi9c-23931
Last seen 8 months ago

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!

r normalization • 170 views
ADD COMMENT
0
Entering edit mode

Hello lakshmi9c!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

PS: You've already asked this question 11 days ago, and received numerous responses.
ADD REPLY
2
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 362 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6