Question: How to analyze differentially expressed lncRNA from total RNA
1
gravatar for ta_awwad
2.3 years ago by
ta_awwad230
Frankfurt am Main
ta_awwad230 wrote:

Hello everyone, I have RNA-seq data and I would like to detect differentially expressed lncRNA with DESeq2, does anyone have analysis workflow to follow? thanks much Tamer

lncrna rna-seq deseq2 • 2.1k views
ADD COMMENTlink modified 2.3 years ago by EagleEye6.4k • written 2.3 years ago by ta_awwad230
1
gravatar for EagleEye
2.3 years ago by
EagleEye6.4k
Sweden
EagleEye6.4k wrote:

Check this post for workflow

A: Any One please provide protocol for Analysing long noncoding RNA illumina NGS da

Ad for R Differential Expression steps in R,

A: Differential gene expression using R studio

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by EagleEye6.4k
0
gravatar for WouterDeCoster
2.3 years ago by
Belgium
WouterDeCoster40k wrote:

I think the most appropriate method is to analyse the data just like you would for all RNA-seq, and filter out the lncRNAs after you get the differentially expressed genes from the full analysis. Preselecting genes will only bias your results.

ADD COMMENTlink written 2.3 years ago by WouterDeCoster40k

Thanks much, do you know by any chance how to get a list of lncRNA transcript (from phantom project ) or I should rely on UCSC lincRNA table? moreover, do you have R code for the filtering step?

thanks much

ADD REPLYlink written 2.3 years ago by ta_awwad230
1

Ensembl Biomart allows you to download what you need.

First: select what is needed e.g. Dataset: Ensembl 89 + then choose species --> Filter: gene type --> lincRNA --> Attributes: Gene ID, Gene Name, Gene Type

Second: Click "results"

Third: Export all results to TSV --> Go

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by YaGalbi1.4k

I'd think the default UCSC/Ensembl annotation will contain already a bunch of lncRNAs, you could complement these if you like with e.g. Lncipedia data.

moreover, do you have R code for the filtering step?

That's quite basic R, see for example here

ADD REPLYlink written 2.3 years ago by WouterDeCoster40k
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