9
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Biological meaning of read length
The read length has absolutely nothing to do with what you are sequencing. It is a characteristic of the sequencing technology you use. NGS sequencing techniques typically produce this sort of short ...
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8
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How to convert FASTQ file format into GTF file format?
You should really read about both these file formats. As swbarnes mentioned, FASTQ and GTF hold different kind of information. GTF stores the annotation of a reference sequence. For example a GTF for ...
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7
votes
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Where to find E.coli gene expression data?
There are some databases in which you can search for E.coli gene expression data:
GenExpDB: E. coli Gene Expression Database
Many Microbe Microarrays Database (M3D): A resource of microbial
gene ...
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7
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Why is the GenBank entry for the genomes of RNA viruses like coronavirus written as DNA?
It would appear that the current policy at GenBank is to represent all genomic sequences as DNA, even though this is not made explicit in any of the easily retrievable documentation on their website ...
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6
votes
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meaning of the "reads" keyword in terms of RNA-seq or next generation sequencing
In RNA sequencing, the RNA is fragmented, DNA is synthesized complementary to the RNA fragments, which is followed by a complementary strand synthesis. Fragmentation can be done after the cDNA ...
- 35.2k
6
votes
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The meaning of RNA-seq data
RNA-seq data usually provides a snapshot in time of the transcriptome of that which is being sequenced. Single-cell sequencing is possible, but less common than RNA-seq on a sample (containing many ...
6
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What is the best method to check for differential gene expression in large dataset? I want to identify aging differentially expressed genes
A standard pipeline for DGE would be Salmon for (pseudo)mapping + DESeq2 for statistical analysis.
Salmon is one of a set of modern, fast and accurate mapping software. Requires a transcriptome to be ...
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5
votes
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Tools to analyze RNA-seq data
You will likely need a tool to "map" the reads on the reference genome.
You may find such a reference genome, together with annotations, here:
ftp://ussd-ftp.illumina.com/.
Mapping tools such as ...
- 2,185
5
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What are the reasons for using oligo-dT instead of oligo-U to isolate mRNAs?
Note - This answer only covers the comparison of rA-dT (RNA:DNA) and rA-rU (RNA:RNA) duplexes, and not more exotic options involving deoxyuridine (dU) and ribothymidine (m5U).
I can think of three ...
- 8,206
5
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What is the difference between 4th generation sequencing and NGS?
I think that all of this is pure marketing and can be safely ignored. There is no basis for the generations of sequencing in chemistry or instrumentation, except possibly that second-generation (...
- 8,528
4
votes
Genes-of-interest analysis between organisms
In RNA sequencing, total RNA is extracted, then mRNAs are purified out from the sample using polyT columns (since mRNAs have a polyA tail, this will attach to a polyT DNA chunk that is attached to ...
- 3,098
4
votes
What is the frequency distribution of each base in a DNA sequence?
The frequency of the bases in the genome isn't equal to 0.25, the frequency depends on what kind of organism you mean. However let's take a look at some of them:
bacteria, most of the time we can see ...
- 2,370
4
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determining meaning of basic biological keywords about C. elegans
Have you discovered wormbase yet? It will become your new best friend. In worms gene names reflect the loss-of-function (lf) phenotype. Daf means "abnormal DAuer Formation," so daf-2 was the second ...
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4
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Why analyse transcriptome instead of proteome?
Q: Why not just extract the proteins…
A: It’s not just a question of extracting the proteins, you would need to separate them and then isolate each of them. There is currently no practical way to do ...
- 23.3k
4
votes
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Confusion about read counts distribution in RNA-seq
Textbook example of multinomial distribution is multiple dice toss. The fair dice has following probabilities:
...
- 573
3
votes
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ChIP-seq for histone modification not in agreement with RNA-seq for expression
It is difficult to draw any conclusion without further experimentation. There may be many other factors that prevent the expression of the gene including factors like post-transcriptional regulators. ...
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3
votes
How to predict a mRNA secondary structure with a large sequence?
Yes, the structure predicted by splitting up the sequence may not represent the actual structure of the full-length RNA. A simple hypothetical case would be that of an RNA whose 3' and 5' UTR interact ...
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3
votes
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What do HG and NA mean in Geuvadis project RNAseq sample labels?
If you google HG00105, among the first hits is geo accession GSM649517 with the title HG00105/NA12878.
Channel1:
...
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How to convert FASTQ file format into GTF file format?
The Tuxedo Suite (Tophat, Bowtie and cufflinks) used to to process RNA_seq data, assuming that is the origin of your .fastq files, should work for you.
https://ccb.jhu.edu/software/tophat/index....
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How to convert FASTQ file format into GTF file format?
Your question is not very clear. What should the contents of your GTF file be? Typically, GTF files contain information about where exons are located in a set of DNA sequences. Determining the ...
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3
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How to convert FASTQ file format into GTF file format?
A fastq contains sequences. A gtf contains coordinates of where features like exons fall in a reference sequence. You can't interconvert them, that makes no sense.
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Tools to analyze RNA-seq data
While I also agree @bli that R and Python (in particular Bioconductor) have more than enough packages for you to compare gene expression. You shouldn't align your ...
- 1,009
3
votes
correction of read counts for spikes
The most common and simplest normalization method for spikes is the Total Count Normalization. It's actually what you're doing here, so what you're doing here is correct. TCM is a useful algorithm for ...
- 1,009
3
votes
Biological meaning of read length
My understanding is that if the reads come straight from the sequencing machine, they will all be the same length. That corresponds to the number of sequencing cycles that the machine was set to ...
- 2,185
3
votes
Correct structure of RNA
Both figures include A,G,T,C.
Those are abbreviations for the bases adenine, guanine, thymine and cytosine.
RNA does not contain thymine, but its unmethylated form uracil, abbreviated with an U.
...
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3
votes
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?
I think your question is:
Can you diagnose someone with an RNA virus by looking for that RNA in their blood?
The use of nucleic acid tests, or NATs in diagnosis has been around for a long time. ...
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3
votes
Why analyse transcriptome instead of proteome?
Why not just extract the proteins and sequence them, quantify them,
analyse and draw conclusions?
Because proteomics is really hard. To provide one example, there is no protein equivalent of PCR. ...
- 3,131
3
votes
RNA sequencing and taxonomic analysis of gut microbiome
The article that you link to clarifies in the methods section that there are two different extraction protocols employed, one for 16S information (probably DNA extraction) and one for total RNA. In ...
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snRNAseq vs scRNAseq in cancer
This is a very interesting question and I will give you an outline of the scenario I think is most likely.
I'm using the same hypothesis to explain another common observation in single nuclei RNA-Seq: ...
- 196
2
votes
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Iron metabolism in the brain
Many articles focus on the pro-oxidant function of iron (and globins in particular). It makes sense that levels may be higher in the CNS due to their role in respiration, which is increased secondary ...
- 407
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