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Determining the sequence of RNA. This technique is used for discovery and quantification of mRNAs and ncRNAs.

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5answers
110 views

Why analyse transcriptome instead of proteome?

Analysing the transcriptome (RNA-Seq, microarrays, qPCR etc) is probably the most widely used technology to assess gene expression and dynamic cellular processes. The results are then extrapolated (...
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0answers
14 views

How many samples to run an association study on B-Cell receptors

We are trying to find biomarkers on the B-Cell receptor VDJ regions. To do this we plan to run Single cell RNA-Seq (using the solution from 10x genomics https://www.10xgenomics.com/solutions/vdj/) to ...
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0answers
7 views

Micro-RNA host genes in RNA-seq

I am wondering if expression of microRNA host genes are determined be RNA-seq? I know actual micro-RNAs are not but I am wondering if their host gene can be. Thanks, Zara
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0answers
10 views

Housekeeping and stably expressed genes qPCR

I am trying to find the most stable reference genes in order to use in qPCR assays. For this I picked 2 genes from RNA seq data and 2 genes EF and GAPDH. From these 4 genes I want to pick two genes ...
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1answer
17 views

Metatranscriptomics Extraction

I am attempting to perform metatranscriptomics analysis of a cleanroom. The DNA input is known to be rather low (<1pg). Despite this, I want to still attempt to try it. I am thinking it might be ...
1
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1answer
44 views

If a person is infected with an RNA virus what percentage of the RNA in the blood of the person contains RNA of the virus?

Karius uses DNA sequencing of everything that's contained in a sample to detect all bacteria and DNA-viruses in the sample. Given the way that costs of sequencing are falling this approach seems to be ...
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0answers
35 views

Why did protocell division coincide exactly with RNA replication?

I know that, in the RNA world, it has been suggested that the first protocell formed by a hollow liposome structure encapsulating an RNA molecule. However, from then on it becomes confusing: I've ...
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2answers
39 views

Correct structure of RNA [closed]

Of the 2 figures, which is the correct structure of RNA, This is the link : 1: https://i.stack.imgur.com/IYgyv.jpg Sorry, the figure is not to scale. If there's any problem with the question ...
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0answers
22 views

RNA contains Uracil in place of Thymine [duplicate]

Thymine does not present in RNA but DNA containing thymine why
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1answer
16 views

dbSNP clarification

I am currently going through this paper - link. In their methods section the authors have described they have used dbSNP for checking biallelic expression of genes. I would like to know if dbSNP ...
1
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0answers
30 views

Should I use glycogen in isopropanol to precipitate RNA or does glycogen have harmful consequences on downstream protocols such as RNA seq?

I have heard that one can use glycogen in isopropanol to better visualise the RNA pellet after centrifugation. What are the advantages and disadvantages of adding glycogen in isopropanol for RNA ...
0
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0answers
17 views

Incomprehensible Bioanalyzer profile

I have extracted RNA from about 4000 C. elegans worms today, using my Trisure and phase-lock gel protocol. The ratios at the Nanodrop are excellent, indicating that there is not protein or salt ...
1
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1answer
88 views

Should I use RNAseZAP on my bench and pipettes before RNA extraction?

Should I spray RNAseZAP on my bench and pipettes before working with RNA? I am regularly using RNase at my bench and would like to work with RNA as well. Could traces of RNase on my equipment degrade ...
1
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1answer
49 views

Where is DNA during the process of RNA extraction using Trisure?

Where is DNA during the process of RNA extraction using Trisure described here? Given that DNA is also a nucleic acid, should I expect the isolated RNA to also contain DNA? However, Bioline claims RNA ...
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0answers
115 views

Is DNase treatment necessary before RNA sequencing?

Is it necessary to treat total RNA with DNase before sequencing it? In particular, if the library prep relies on a poly-A enrichment, is it necessary to remove DNA, knowing that genomic DNA does not ...
0
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0answers
27 views

Why is a T-to-C change assumed to be A-to-I in RNA-seq data? (RNA editing)

I understand that the mechanism of A-to-I change is deamination of adenosine (A) by one of the ADAR enzymes and that this resulting inosine (I) nucleotide is translated as a guanine (G) by translation ...
0
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0answers
141 views

What mutations in the DNA replication machinery would decrease the length of Okazaki fragments?

I just started learning about DNA replication and came across an interesting thought. I know that Okazaki fragments are about 100-200 nucleotides long for eukaryotes, yet if a cell was mutated, is ...
2
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2answers
177 views

Which information can be extracted from time course RNA-Seq Data?

So I am very new to the area of biology so I am sorry if this is a stupid question. I have RNA-Seq data carried out over a span of 100 days and I have gene expression data in the following format. ...
0
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0answers
29 views

Example RNA-seq dataset with high false positive rate

I am trying to obtain an example RNA-seq dataset that has a verified high false positive rate. For the most part, I am hoping to examine these false-positive DEG calls and see what they look like. ...
1
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0answers
20 views

RNA extraction from soil

I have been trying to extract RNA from soil without success. I have used commercial kits (The Plant DNeasy kit) because I did not want to buy a complete new kit (Soil) to do 5 extractions. Is there ...
0
votes
1answer
55 views

de novo assembly applications

Hey I hope this question supposed to be in this forum. I'm not from the biology community, I'm from the data security community so im not familiar with the words you might use for answers I need to ...
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0answers
55 views

The advantages of using a strand specific cDNA in RNA-Seq?

May I ask what are the advantages of using a strand specific cDNA library in an RNA-seq experiment? as far as I know it can make us able to read the code region but what about other advantages?
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1answer
52 views

Is my RNA-seq experimental design correct to use it for SNP calling?

I am a newbie here and would highly appreciate your advice about one particular experimental design. We have data from RNAseq experiment which was originally designed to assess differential ...
7
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2answers
745 views

Biological meaning of read length

I have some FASTQ files in two datasets which are sequences from 16Srna region. The first dataset is amplicons form V4 region and the second is V3-V4 region. However all the reads are 250 nucleotides ...
2
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0answers
29 views

When to decide that two similar sequences are different genes or not?

Working on RNA-Seq data directed me to ask this question. In RNA-Seq jobs, after de novo assembly we have lots of transcripts with different rates of similarity (0 to almost 100 percent) that we ...
0
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1answer
122 views

16s rRNA Sequencing From Gut Microbiome (stool)

Do I extract RNA or DNA from gut microbiome (stool samples) if want to do 16s rRNA sequencing?
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1answer
110 views

the meaning of “Non-primary hits” and “tags”

Can I ask you to help understand the meaning of "Non-primary hits" and "tags" in the following paragraph related to RSeQC: The result table reports total number of reads (excluding nonprimary hits) ...
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1answer
225 views

What is the meaning of the word 'bin' in the context of RNA-Seq?

I have a question from a book about RNA-Seq. I would like to know the meaning of the word "bin" in the below cited paragraph: RseQC has several nice features not found in the other programs: (a) ...
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1answer
193 views

Which are the best programs to analyze circular RNA?

Hello I'm just started with bioinformatics and I would like to know which programs are best for the task of finding circRNA (circular RNA) in sequences of tissues and different cellular types. I have ...
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0answers
29 views

Blastx: from gi to description

I have done a blastx and use the outfmt 6 option, because I want to work in the tables format. When I do this I get subject ids of the type sp|Q7XJS0|ASHR1_ARATH, sp|Q39547|CUCM1_CUCME, et cetera....
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1answer
83 views

How do I read an RNA expression pattern?

When reading about diseases one can find links to proteins and their associated genes, an example of which is here. I'm wondering how to decode/read the following graph as a non-specialist in this ...
3
votes
1answer
77 views

correction of read counts for spikes

I have 4 RNA-seq samples (1st is control and the other 3 are treatments) and 5 spikes. I used different concentrations for 5 spikes but over different samples, I used similar concentration. for ...
2
votes
2answers
73 views

How much tissue is required to do RNA-seq analysis on a single organism?

How much tissue would be required to do RNA-seq analysis on a single organism? More specifically, if a person wanted an RNA-seq analysis of expression for a single organ, how much tissue would they ...
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1answer
165 views

Multiple transcripts matching same gene in de novo assembled RNA-seq data, but FPKM values vary?

I have a data set of de novo assembled RNA-seq datasets across different sample types. When BLASTing, many of the matches of the individual transcripts match to the same gene on the reference genome. ...
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1answer
49 views

where i can download reference MSU7 rice genome?

I am working with RNA Seq data analysis. I have to download MSU7 rice genome. somehow i downloaded from "http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/...
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1answer
26 views

RNA seq: Should non-infected units be used for RNA-seq?

I am designing a RNA-seq experiment to study transcriptomic profile changes upon parasite exposure. Some papers I read, mostly extract RNA from the entire treatment group (organisms exposed to ...
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0answers
41 views

Can I modify the RPIX primers for MiSeq Sequencing?

I am in the process of making a 48 sample pooling library prep, and I am about to order the RPIX primers for Illumina MiSeq sequencing. The primer is like this P7 - i7 Tag - UNKNOWN - RA3 example ...
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1answer
39 views

What determines the amount of data you would get from a sequencing experiment?

When someone performs a sequencing experiment, what determines how much sequencing data you get from the machine (Illumina, PacBio, Nanopore, etc). Or maybe, put differently, how does the machine know ...
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1answer
51 views

What factors should I consider when selecting a reference genome for mapping?

I am under the impression that the most recent reference genome is typically the best case. What other things should I consider when selecting a reference genome? For example, is there any particular ...
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4answers
312 views

Tools to analyze RNA-seq data

I hope this is a good place to ask such question. I have to do some data analysis on RNA-seq data from human cells. I am currently searching for tools to help me with that. Specifically, I would need ...
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0answers
49 views

RNA-Seq library normalization and experimental setup

I'm working on an RNA-Seq project and I am trying to figure out library normalization. I'm aware of using the geometric means (e.g. cuffdiff) of the fpkm for the normalization. However, I was ...
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1answer
73 views

Do house keeping genes vary across tissue

I am working on an RNA-Seq project, and I am aware that some researchers use housekeeping genes as a method of normalization. My project has several different tissues, and I was wondering if ...
2
votes
1answer
131 views

Do all microRNA isoforms need to be known and sequenced to obtain microRNA expression?

From what I understand, microRNA are short "hairpin" shaped nc structures. When sequencing and counting miRNA, isoform miRNA are "found" which are subsections of varying length and possibly with some ...
2
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2answers
71 views

Is it possible to identify a particular gene sequence from next gen sequencing techniques (especially RNA-seq )?

I have to check the expression of a gene in a fish whose sequence is not known in the fish in question. Sequence is known in an another fish (zebrafish) but the gene has 10 isoforms. The genome of ...
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0answers
40 views

Is it okay to scale the RNA-Seq counts after log-transformation?

On an RNA-Seq dataset, I want to apply a clustering algorithm which requires zero-mean uni-variance gene expression levels. I am wondering whether it makes sense to use "scale" function in R after ...
0
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1answer
51 views

How do you obtain specific mRNA transcript levels for comparison from a Hi-Seq dataset?

I have HiSeq data from mice exposed to two conditions. I would like to answer the following question: "Is there a significant difference in mRNA transcript levels when comparing condition A to ...
2
votes
0answers
116 views

What is the another use of de Bruijn graphs in bioinformatics except DNA assembly? [closed]

I implemented own generic de Bruijn graph, which I use for DNA assembly (alphabet: A, C, G, T). I try to find purpose of de Bruijn graph for another bioinformatics problems, if some exists. I want use/...
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2answers
747 views

What is the most appropriate way to normalize gene expression data?

This question comes because reading a paper about normalization of gene-expression data, is not clear if the method for normalize the data is just for RNA-Seq data or could be applied also for ...
0
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2answers
697 views

What is the frequency distribution of each base in a DNA sequence? [closed]

Can we say that the frequency distribution of each base in a DNA sequence is equiprobable? After the negative answer; i rephrase: Is there a use case in which the frequency distribution of the bases ...
2
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1answer
157 views

Questions on adding a protein to a DNA library [closed]

Two questions regarding finding the DNA sequence of a amino acid sequence (AA): 1) If you are able to find out the mRNA sequence of an AA, then don't you automatically know the DNA sequence? 2) ...