Bulk RNA-Seq data analysis

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6.5 years ago

saumya001 ▴ 10

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 • 3.1k views

ADD COMMENT • link 6.5 years ago by saumya001 ▴ 10

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You can try GeneSCF.

ADD REPLY • link 6.5 years ago by GenoMax 142k

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

ADD REPLY • link 6.5 years ago by Friederike 8.9k

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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 REPLY • link 6.5 years ago by saumya001 ▴ 10

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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