Question: Bulk RNA-Seq data analysis
1
gravatar for saumya001
17 months ago by
saumya00110
saumya00110 wrote:

Hi, I have tissue RNA-Seq data of both healthy and diseased samples. I have done differential analysis using DESeq2 and have the differentially expressed genes list. I am trying obtain the GO terms related to those genes usisng DAVID. Could anybody suggest some other tool to add functional annotation to my gene list. I am quite new to this field and i am rather confused what other kinds analysis except DGE analysis can be done on bulk RNA-Seq data. Please suggest some.

Thankyou

rna-seq • 1.2k views
ADD COMMENTlink written 17 months ago by saumya00110
1

You can try GeneSCF.

ADD REPLYlink written 17 months ago by genomax65k
1

the analyses you're going to do should ideally be guided by biological questions. what were the reasons to generate that data?

ADD REPLYlink written 17 months ago by Friederike3.7k

Well I wanted to work towards the difference between healthy and diabetic samples. I started out gradually by doing DGE to know the up and down regulation of genes between them. Now I would like to go for clustering I guess to know if the samples would cluster according to the sample type or any other type. But I am not really sure if I should do that. Any suggestions would be a great help

ADD REPLYlink written 17 months ago by saumya00110

if the samples would cluster according to the sample type or any other type

@Kevin has a nice tutorial that you could use for that: A: PCA plot from read count matrix from RNA-Seq

ADD REPLYlink modified 17 months ago • written 17 months ago by genomax65k

Thankyou so much !!!

ADD REPLYlink written 17 months ago by saumya00110
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