Poly(A) tail 5'/3' bias
Is the abundance of Poly(A) tail (A^25), in sample isolated using poly-A mRNA, potentially caused by a 3' bias in the isolation ?
Could using uneven specimen cause bias in analysis (even when filtered)?
rna-seq
rna-seq
sequencing
• 1,713 views
•
link
updated
by
GenoMax
16K
• |
written
by
biostar.anon
0
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
BULK mRNA-seq with UMIs. Do I need to normalize by gene length?
written by txema.heredia 31Hi, I am analyzing some BULK mRNA-seq data that included UMIs during the sequencing. I don't have much experience analyzing bulk RNA-seq, and it is …
-
Uneven coverage of reads - ChIP-Seq
written by Genestar 0Hi Everyone, I have sequenced ChIP samples (Input and IP) - 1X75 bp, 10M depth. DNA shearing was done using sonication (Bioruptor). Once I map …
-
RNA-seq of human cells and bacteria
written by bart 5Hey, 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 …
-
Poly-A trimming - is it necessary?
written by ika 5I see poly-A trimming listed as a recommended step in many RNA-Seq protocols. However, I can imagine that trimming e.g. all As from the ends …
-
How to design qPCR primers to validate RNA-seq experiment?
written by brett.vanderwerff 3Hello, I did a bulk mRNA-seq experiment where I treated human cells in vitro with control of drug. I am only interested in determining differential …
-
Cause of 3' bias in polyA selection step in RNASeq library prep
written by rnaseqbias 0Hello. What is the cause of 3' bias in the polyA selection step in RNASeq library preparation? (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4310221/figure/F6/) I have searched around on the internet …
-
Reasons for polyA in RNA Seq Reads
written by DVA 64In my poly A capture RNA sequencing fastq output, I noticed that about 20% of the reads contain poly A in the middle (or even …
-
HiC interactions has a bias towards even numbers
written by ingerslev 0The data being analysed is a capture Hi-C dataset looking at the captured promoters in relation to a predefined set of enhancers. The reads were …
-
Search for high quality service provider for RNA-Seq including statistics
written by achimbell 0Dear people at Biostars, We assume a lot of you have already experiences with companies providing RNA-Seq services. One of the main problems we observed …
-
3' Bias in RNASEQ data
written by mjg 3Hello, I have rna seq samples which show 3' bias in the gene body coverage of 10,000 random genes. I first looked at the RIN …
You need to be a bit more specific - I'm not sure what you are asking...?
I am asking if a overabundance in poly(A) sequences (>1%) in RNA-seq data of a sample could be caused by RNA break during isolation (thus resulting in a 3' bias).
I found a specimen file with an overabundance of A* sequences in fastqc compared all other specimens.
Second, even when filtered for poly(A), tail would such a bias affect DE analysis ?