Question: How to get RNA data from whole genome sequencing data
0
gravatar for rick42
8 months ago by
rick420
rick420 wrote:

Hi,

I am studying bioinformatics, non-biological major.

I encountered some problems in reproducing the results of a paper. The DOI of this paper is 10.1007/s10753-019-01060-8.

This paper analyzes circRNA, miRNA, and mRNA of rats, but it uses whole genome sequencing. I tried to deal with it myself but failed.

I downloaded the reference sequence and annotation file of the rat, the URL is this , but I don’t know if it is correct?

I searched a lot of data on whole genome sequencing processing on the Internet, but most of them were doing mutation analysis.

I want to know how to get RNA data from whole genome sequencing data.

Thank you.

ADD COMMENTlink written 8 months ago by rick420

From a quick look at the paper here, it looks like a standard RNA seq + DEG paper with the sequences deposited in the SRA under PRJNA527717. Not sure what it is your after as there doesn't seem to be any whole genome sequencing.

ADD REPLYlink written 8 months ago by Jean-Karim Heriche24k

What they are writing here is whole genome sequencing, how do I judge what type it is?

ADD REPLYlink written 8 months ago by rick420
1

SRA is an uncurated data resource. The study type is part of the metadata submitted by the authors and in this case is wrong. The authors seem confused about the use of the term whole genome sequencing.

ADD REPLYlink written 8 months ago by Jean-Karim Heriche24k

I guess you refer to

Utilizing whole genomic next-generation sequencing, we compared the DE circRNAs and miRNAs between sepsis and control groups.

They did an RNA (expression) study, not whole genome DNA sequencing. Poor choice of words, I agree.

ADD REPLYlink written 8 months ago by ATpoint44k

Yes, they also wrote whole genome sequencing here, so I am confused.

In addition, I want to know, is the reference gene and annotation file I am looking for correct?

ADD REPLYlink written 8 months ago by rick420
1

As said, poor choice of words, no WGS seems to be available. Yeah, NCBI reference is ok, alternatives could be from Ensembl. Probably does not make much of a difference, I personally prefer the Ensembl nomenclature though (actually GENCODE but this only exists for human and mouse).

ADD REPLYlink written 8 months ago by ATpoint44k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2191 users visited in the last hour
_