Consensus on poly-a selected lncRNAs for differential expression analysis · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Consensus on poly-a selected lncRNAs for differential expression analysis

Hi all,

This is somewhat related to my previous question: I was wondering if there is a general consensus on the validity of poly-a selected lncRNAs for DEA. Would this have scientific value? Or would it always be better to perform whole transcriptome sequencing for something like DEA of lncRNAs?

Thanks!

lncrna

• 1,172 views • link

updated 4.8 years ago by Carlo Yague

• written 4.8 years ago by bart •

1 answer

Some lncRNA are polyadenylated, others are not. If you want to analyse all lncRNA, it is best to perform whole (or ribodepleted) transcriptome sequencing. That being said for the lncRNA for which there is sufficient signal in poly(a)-seq data, you can still perform DEA while keeping in mind the limitation that you might be missing some non-poly(a) expression signal.

• 0 views • link

written 4.8 years ago by Carlo Yague

Log in to answer this question.

More posts like this

WGS for CNV and Aneuploidy analysis
written 1.3 years ago by bioinfo1990 •

Hello, I’m planning to run whole genome sequencing on sheep cells for CNV and aneuploidy analysis. I’m wondering what sequencing depth is typically recommended, how …
Computational way to distinguish between polyA and total RNA bulk RNA-seq
written 1.6 years ago by predeus

Hi all, I was wondering if you know any published method that could allow one to identify if the bulk RNA-seq experiment in question was …
MetaTranscriptomics amount of viable reads
written 2.0 years ago by zjhennin •

Hey all, I have a more scientific question in nature. Essentially, my group has done meta-transcriptomics for the first time in our lab and we …
Differential expression analysis with very high duplication rate
written 2.5 years ago by JMB •

Hi, I am doing a DE analysis on an RNA-seq dataset and have a question about PCR duplicates. The organism is a bacteria with a …
Can a heterogenous approach to data normalization yield a better consensus learning result?
written 4.5 years ago by fuellen •

dear All, The following makes sense intuitively, but I cannot find a reference: - Let's say I've got 3 datasets, for example differential gene expression, …
Differential expression analysis (DEA) of lncRNA
written 4.8 years ago by bart •

Hi all, I'm relatively new to RNA-seq analysis and want to perform differential expression analysis (DEA) of lncRNAs. I have read multiple different protocols and …
RNA-seq of human cells and bacteria
written 5.2 years ago by bart •

Hey, I want to study bacterial RNA which may be present inside human cells. The transcriptome of the human cells have been studied using RNA-sequencing …
question regarding histone and lncRNA genes in poly(A) RNA-seq data
written 5.5 years ago by Alex V. Gopanenko •

Dear community, I want to ask a question regarding the presence of histone and lncRNAs genes in poly(A) RNA-seq data. I know that some of …
Queries regarding RNASeq sequencing
written 6.8 years ago by glady

Hello all, I have some very simple questions regarding Human transcriptome sequencing: 1) Which library size would be better for sequencing: 1x150 or 2x75? 2) …
Worthwhile to upgrade BWA in NGS pipeline?
written 7.7 years ago by BCArg

We are currently using BWA (v0.7.10) as the aligner algorithm in our NGS pipeline. To summarise, we perform whole genome sequencing (WGS), whole exome sequencing …