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

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3
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2answers
55 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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0answers
11 views

How can I apply any machine learning model/classifier on miRNA seq data?

I recently got micro RNA sequencing data from the TCGA. I am currently trying to early detect Mesothelioma. How is microRNA seq data different from microRNA expression data? MicroRNA expression ...
0
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2answers
67 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 ...
0
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1answer
31 views

Which is the proportion of metagenomics reads that cannot be mapped in any genome?

I was wondering if anybody knows how many reads from metagenomic or metatranscriptomic data do not map to known sequences and are therefore unidentifiable? I found a figure for viromics, which seems ...
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0answers
33 views

Extracting the donor/acceptor sites from mRNA sequence(PERL/ DNA transcription)?

I have the following program that I am analyzing and trying to understand. Overall purpose of it is to put out, based on the option selected, the set of introns, exons, acceptor sites , or donor sites ...
2
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1answer
54 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) ...
0
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4answers
230 views

How to convert FASTQ file format into GTF file format?

I have a plenty of FASTQ files (FASTQ is a standard for storing the output of high-throughput sequencing instruments such as the Illumina Genome Analyzer) and need to convert them to GTF format (gtf - ...
0
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1answer
37 views

Why are some genomic regions sequenced more than the others?

We have to normalise read count data from RNA-Seq experiments in order to account for the fact that some genomic regions are mapped more than others. i.e. we get the tags per million reads (TPM). In ...
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0answers
21 views

Cell specificity RNASeq [closed]

I am working on finding the cell specifity information (eg. Epithelial cells, muscle cells etc) from RNASeq data of colon tissue. I was referring to CellCODE but that is related to PBMCs. Does anyone ...
1
vote
1answer
41 views

amount of tRNA and its extra arm

How much of the total RNAs is tRNA? Some say 15% and some 20%. Those percentages came from my different teachers. Which is correct? And what are the functions of the extra arm (variable loop) of tRNA? ...
1
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0answers
20 views

Can we take advantage of nanopore sequencing systematic errors to predict secondary structure motifs?

One of the methods of single-molecule sequencing, Nanopore sequencing, is based on traversal of DNA strand through a nanopore. Nucleotide is determined by measurement of ion current (when nucleotide ...
3
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2answers
52 views

ChIP-seq for histone modification not in agreement with RNA-seq for expression

I have ChIP-seq for H3K79me2 and H3K36me3 and RNA-seq data for treated and untreated samples. Those two histones mark active genes. Lets say, hypothetically, a peak caller finds differential sites at ...
2
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2answers
533 views

Using RNA-seq to compare gene expression across patients instead of between Control and Experimental conditions

I am working with RNA-seq data from the Cancer Genome Atlas TCGA and I have been reading about how people have compared gene expression levels measured by RNA-seq. Many of the papers I have read talk ...
0
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0answers
26 views

GC-Content bias and length bias in TCGA RNA-seq level 3.0

I want to use RNA-Seq (level 3.0) data from TCGA database in my research. What kind of preprocessing steps I should do? Do I need to correct GC-Content bias and length bias in these data?
3
votes
1answer
57 views

How to predict a mRNA secondary structure with a large sequence?

When I use some web servers to predict a mRNA secondary structure, I find they always required in a small size sequence. If I use a long sequence and cut it into small parts, do these small parts ...
1
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0answers
160 views

Understanding Illumina Adapters

I am currently working on a project where I need to trim the adapters off of some single end read RNA-Seq data, and I want to know which sequences to cleave. Illumina TruSeq adapters were used. I ...
0
votes
1answer
55 views

What do HG and NA mean in Geuvadis project RNAseq sample labels?

I'm looking at RNASeq Data from Geuvadis website e.g. the file GD660.GeneQuantRPKM.txt.gz. The samples are labeled by e.g. HG00105.1.M_120209_7 or NA20812.2.M_111216_6 What do HG and NA mean? Are ...
2
votes
1answer
104 views

Differential gene expression analysis between species

I have RNA Seq data from mouse and human skin ( 2 replicates each) and want to compare the expression of the orthologous genes to find any which are differentially expressed. I have quantile ...
2
votes
1answer
143 views

How do carrier RNAs increase yield in sequencing experiments?

I would like to know how carrier RNAs increase yield in RNA/DNA sequencing experiments. Is their main function in the precipitation steps of each protocol (i.e. small quantities are difficult to ...
4
votes
2answers
191 views

New GO terms after TopGO enrichment? [closed]

I ran an enrichment analysis with custom annotations using TopGO and surprisingly I obtained new GO terms inside the significant GO terms. Is that possible? The only reason I can imagine this is ...
1
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0answers
39 views

Getting read size less then specified in parameter file Flux Simulation

I have tried to use flux simulation tool to generate simulated RNA-seq data. I gave the following parameter file to flux-simulation shell script ...
4
votes
1answer
63 views

determining meaning of basic biological keywords about C. elegans

First of all I have to say that I have no biology background since I'm a undergraduate computer science student. Nowadays, for my research I need to use some of the databases related with ...
0
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1answer
45 views

Downstream analysis after in vivo pathogen RNAseq

We performed RNA-Seq of in vivo bacterial samples and identified some key up- and down-regulated pathways. We compared bacteria during infection with conventional agar plate. Which could be the next ...
4
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1answer
181 views

How could I identify whether given RNA-seq data is paired end or single end

I need to have a RNA-Seq dataset and therefore, I've visited the following site NCBI-geo C. Elegans In the Supplemantary file part, I clicked the SRP/SRP051/SRP051702 ftp and downloaded sra file. ...
0
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1answer
96 views

Finding Rna-Seq dataset for C. Elegans (Caenorhabditis elegans)

I want to find a RNA-Seq dataset for C. Elegans to use it in RNA-Skim software. For those who does not know RNA-Skim let me explain it a bit. It is a tool which is used to quantify RNA-Seq data using ...
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0answers
46 views

RT-qPCR of selected differential expressed genes: which dilutions in calibration curve?

I've seen in MIQE guidelines that calibration curves a needed when performing RT-qPCR. I'll use genomic DNA to perform these calibration curves. My question is that I don't know the range of ...
0
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1answer
65 views

What pattern can be learned from the data of RNA seq counts and HiC matrix? [closed]

I now have some data on the RNA seq counts and related Hi-C matrix of gene segment on a chromosome. My concern is, basically, what can we do with these data so as to establish the connection between ...
5
votes
1answer
232 views

Where to find E.coli gene expression data?

I am searching E.coli whole genome expression data with different conditions, any suggestion is appreciated. Condition could be for example different growth temperature, different medias, etc. I have ...
5
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1answer
75 views

Genes-of-interest analysis between organisms

I am interested in identifying the differential expression between several genes-of-interest of different organisms. I am trying to assess the benefits of RNA sequencing over microarrays. Both ...
5
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2answers
217 views

The meaning of RNA-seq data

many papers I read mentioned "RNA-seq data". While searching for the meaning of this word, I could not find any layman's definition. As far as I understand, RNA-seq data is the complete RNA ...
3
votes
1answer
556 views

meaning of the “reads” keyword in terms of RNA-seq or next generation sequencing

I'm an undergraduate student at computer science and currently, I'm interested in bioinformatics. Today, I've started to read a paper about clustering and classification of non-coding RNAs can be ...
6
votes
1answer
332 views

How much total RNA can be extracted from Drosophila brain

I am wondering how much total RNA could be extracted from a single D. melanogaster brain. I could not find this information from the literature. The closest hit was this paper, that claims that ...
2
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0answers
26 views

Gene expression for mouse feeder cells (inactivated MEFs)

I'm looking for a paper with gene expression data for mouse feeder cells, inactivated by gamma radiation or mitomycin C. Ideally I'd like RNA-seq data but I'll use microarray data if that's all there ...
7
votes
1answer
704 views

RNA seq and using of Poly(A) or non-Poly(A) based amplification of RNA

I'm studying "Deep sequencing the circadian and diurnal transcriptome of Drosophila brain" Hughes et al., 2012. I've got some problems with the materials and methods. Before RNAseq, the authors ...
2
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2answers
82 views

During bridge amplification of DNA sequences, why aren't sequences amplified in both orientations?

During bridge amplification, when sequences attached to adapters on the surface form "bridges" and are replicated, it seems like sequences with either end attached to the surface will be created. For ...
7
votes
2answers
588 views

RNA-Seq library construction challenges: the biases of RNA fragmentation vs cDNA fragmentation

I recently watched a presentation on RNA-seq that covered some of the choices one can make along the way, and I didn't fully understand one of the choices in particular. Near the beginning of the ...
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0answers
59 views

3 end RNA seq library construction

I have tried to make cDNA libraries from FFPE tumor blocks (highly degraded RNA) using the 3' end RNA seq protocol provided by West lab. Here is the link for the same. ...
1
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1answer
162 views

Regarding the difference between cDNA library and RNA sequencing (Biochem. technique)

I was wondering why establishment of cDNA library required the step of reverse transcription (i.e. turning the sequence into DNA) why not directly using the extracted RNA for sequencing and converting ...
4
votes
2answers
747 views

Why is assembling paired end illumina without any input parameters an important problem?

In one of the comments in this question about multiple sequence alignment, it was stated @5heikki: btw if you want a good bioinformatics problem, come up with an assembler that assembles any ...
3
votes
1answer
158 views

Should the sum of RPKMs be constant over experiments

I have cufflinks data from 18 different RNA-seq experiments. I've noticed that if the sum all the RPKM values for a particular experiment, are vastly different between experiments. How could this be? ...
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0answers
233 views

Is the default kmer 25 value in Trinity still ok for assembly of 150bp reads from Illumina HiSeq 2500?

I will soon be receiving Illumina HiSeq 2500 data (150bp PE stranded reads). In the past we have been using Trinity as our assembler of choice, but it uses a default kmer value of 25. I believe this ...
2
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2answers
78 views

In genome research, what is the problem in Mapping that may be caused by reads being too short?

In the following scenario: You were given short sequence reads of plant RNA obtained from a next-generation sequencing machine (fragments of 20–30 nucleotides in length). You attempt to map them back ...
3
votes
1answer
143 views

What is meant by single molecule sequencing?

When sequencing papers refer to single molecule sequencing, what is their definition of a "molecule". Are they saying base by base? The entire DNA chain in a chromosome can also be though of as a ...
3
votes
2answers
677 views

How were the first primers made

I keep reading about how primers are useful in pcr -- they allow you to select a specific dna region. Similarly, in NGS or Sanger sequencing they give you a starting point. The primers I see are about ...
4
votes
2answers
219 views

GO terms for non-model organisms

I have a list of differentially expressed genes from an RNA-Seq experiment in Xenopus laevis that I'm looking to functionally annotate with GO-terms. As X.laevis is not listed in DAVID it seems I have ...
3
votes
0answers
93 views

Data analysis of transcriptome sequencing data [closed]

I want to learn more about the data analysis and statistics on transcriptome sequencing data. I would like to read some important papers of the field and books and maybe some MOOCS, if they are ...
3
votes
1answer
2k views

RNA-seq analysis - q-values in cuffdiff

I'm using cuffdiff 2.1.1 to look for differential gene expression between two conditions. Each condition has 2 biological replicates. The results I get look promising from a log fold change ...
3
votes
1answer
81 views

How can chromatin state be measured?

I have some RNA-Seq data and I'd like to align it to the physical genome and see which sections of chromatin are geometrically open and being transcribed. The data are already sequence-aligned, and ...
4
votes
2answers
244 views

Current state of direct RNA sequencing

I had a colleague ask me recently whether mRNAs could be sequenced directly. I found this Nature paper[1] published by Helicos in 2009, in which they describe their developments in the area. It's been ...
3
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1answer
2k views

What is the purpose of Y-shaped adapters in Illumina sequencing?

Y adapters different sequences to be annealed to the 5' and 3' ends of each molecule in a library. The arms of the Y are unique, and the middle part, connected to the DNA fragment, is complementary. ...