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Questions tagged [dna-sequencing]

Technique(s) by which the sequence of DNA is obtained. The principles are similar for RNA-sequencing.

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Comparative cost of RNA-seq vs sequencing full length cDNAs

I am in the process of assembling and annotating the genome of a non-model organism, using almost exclusively short read (paired-end Illumina) data. Throughput is one obvious benefit of these data (...
Daniel Standage's user avatar
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Poly-G tails in NovaSeq Paired-end sequencing from museum samples

I'm currently working with DNA samples originating from museum specimens, this means they have been stored in formaldehyde for the last 50-100 years. The DNA I'm analysing has been sequenced by ...
RAHenriksen's user avatar
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Do eukaryotes assimilate DNA that is floating in the extracellular membrane?

Prokayotes, which replicate primarily using binary fission, don't get much genetic diversity. For this reason, they take in any genetic material they encounter, in a gambit to help them better adapt ...
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Is blood typing still useful for analysis of ancient tissues?

Modern techniques. In recent years, DNA sequencing has become extremely cheap. This, compounded by the ability to PCR miniscule samples to viable samples for analysis, means that aDNA can be extracted ...
James's user avatar
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Which sequence assemblers I can use to compare different paradigms?

I'm a high school student whose interested in bioinformatics. Therefore I chose a project which I study Sequence Assembly. My main goal is to compare different paradigms (Greedy, OLC, De Bruijn). I ...
Bora M. Alper's user avatar
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DNA preservation at room temperature

I am considering preserving the DNA of a family member who passed away. The funeral home offers a service called DNA Memories from a Canadian company (CG Labs). They have two options: Store the DNA in ...
EugeneO's user avatar
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Construct picture of person's face from DNA

Would it be possible to construct a picture of a person's face from his/her DNA?
Siddhartha's user avatar
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How can I create R8 (homopolymer repeat) filter without using illumina pipeline?

illumina instruments have built-in -or online- analysis software for variant analysis (CASAVA). This software can filter out the false positive variants near the homopolymer repeats (AAAAAAAA) and ...
Can H.'s user avatar
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Inter-codon mutations statistical analysis

I am looking for a statistical approach to inter-codon mutations. For example a 64*64 (64*63 actually) table, that contain the possibility of mutation from one codon to another codon (CCA to CAA or ...
MySky's user avatar
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Is double-stranded DNA denatured to single-stranded DNA in retorted canned tuna?

A PCR reaction has a cycle of about 55°C annealing, 72°C extension and 95°C denaturing with short time spans. Retorting canned tuna heats the tuna to 115°C to 121°C for 30 minutes to 2 hours depending ...
A Old Tuna Guy's user avatar
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Are there any barriers to telomere sequencing other than length?

In the comments to an answer on this question, it was noted that long read sequencing methods (e.g., from PacBio or Oxford Nanopore) have largely eliminated repeat-based assembly problems for bacteria....
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What does the final (Illumina) RNA-seq library contain? ss cdNA or ds cDNA?

I guess the oligos on Illumina's flow cell only hybridize to to single-stranded cDNAs (sscDNA). However, when I read the TruSeq protocol (googled: TruSeq® RNASample Preparation v2 Guide) at the PCR ...
MCH's user avatar
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What are haplotype blocks and what is the effect of hybridization on these?

In this PDF, there is a quick definition of haplotype blocks. A haplotype block is a set of closely linked alleles/markers on a chromosome that, over evolutionary time, tend to be inherited ...
M. Beausoleil's user avatar
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totaling OTU from 2 or more observations and assign to new observation in OTU table from qiime

I am new to microbiome processing pipeline but I want to ask, How do I combine two observations and assign it to a new single observation in the OTU table resulted from QIIME. Here is the situation. ...
Bob Adyari's user avatar
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DNA Longevity in Keratin, Ivory and other Bioplastics

For how long is DNA viable for extraction and/or sequencing in bioplastics created by the human body? I checked out a few links online, and this article gives a record of about 7000 years for frozen ...
Albert Perrien's user avatar
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How does one apply Bayesian inference to quantify a read the deeper you sequence?

For NGS sequencing technology, the "deeper" you sequence given fragments, the more certain you are of what is being sequenced. This sounds like a simple application of Bayes's Rule. What is the ...
ShanZhengYang's user avatar
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362 views

RAD sequencing: choosing the appropriate enzyme?

I’m studying Darwin’s finches genome and I say in some articles that the researchers used restriction enzymes to cut the DNA in their double digest RAD protocol. They are using EcoRI and MseI (GAATTC ...
M. Beausoleil's user avatar
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How to identify genes in Ralstonia that synthesize PHB and promote granule formation?

The compound polyhydroxybutyrate (PHB) is of considerable industrial interest as a biodegradable substitute for plastic. PHB is synthesized from glycerol by the bacterium Ralstonia eutropha. PHB ...
xxx222's user avatar
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Can Pfx polymerase add only one 3' A overhang?

I am trying to clone a PCR product that was amplified using Pfx polymerase into pGemT vector. I had to A-tail the PCR product using Taq polymerase since Pfx only generates blunt end products. My ...
pepe84's user avatar
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Reverse complement of reconstruction model for assembling reads

One way to assemble fragments produced by DNA sequencing (often called reads) is to seek for the shortest common superstring that contains all the reads of a given set of reads. One model for this ...
Heidi Garcia's user avatar
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Predicting how proteins will be cleaved

Is it possible to predict how proteins coded from mRNA will be cleaved? The reason I was interested in this is because I did some initial work to translate the raw Coronavirus RNA sequences, which you ...
Imran Q's user avatar
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What are the advantages of long read sequencing for cancer oncogenomic research?

Currently I am using whole genome nanopore sequencing, Illumina short read and 10x linked read to study oncogenesis mechanisms of certain types of rare cancer. I am wondering about the advantages of ...
mike's user avatar
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Why can DNA tests with mixed DNA of several people not be used to detect a criminal in a database?

Scenario: Two males attack another pair of two males with a weapon. The attackers are fought off and the weapon remains. Why does the police require DNA samples of the two who have been attacked to be ...
pascalwhoop's user avatar
1 vote
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How to determine which allele GRCh37 has?

is there a website where I can search GRCh37 by location or rs IDs, to determine which allele it has at a specific location? I think http://grch37.ensembl.org/ might be the answer to my question, but ...
krstn's user avatar
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Hardy–Weinberg equilibrium for SNPs

I have a SNP stats file structure, which contains all information about genotypes and imputed SNP/INDEL imputation qualities, allele frequencies and minor allele assignment. ...
user2340939's user avatar
1 vote
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39 views

Single-cell ATAC seq arrays

As part of a data analysis project, I encountered two kinds of single-cell assays for transposase-accessible chromatin using sequencing (single-cell ATAC seq) methods. The first uses combinatorial ...
youngtableaux's user avatar
1 vote
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How diverse are the sperm cells of an individual male due to random mutations?

Due to the sheer number of sperm cells in an individual and the rate of mutations, are they likely to be incredibly diverse and encompass most of what we see across our species? For instance would it ...
Logan545's user avatar
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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 ...
charlesdarwin's user avatar
1 vote
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49 views

Replication cohorts in microbial GWAS

Replication in an independent cohort is of course the gold standard in GWAS studies, and many high profile journals will now (quite rightly) not accept finding indicating a phenotype genotype ...
user33904's user avatar
1 vote
0 answers
36 views

What are the exact reason causing missing calls in a VCF file from exome sequencing?

My data is a VCF file from exome sequencing variant call. I'm not very familiar with the sequencing process and variant calling process. I noticed that there are some missing genotypes, which is ...
Yan's user avatar
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199 views

VCF files - examples for haploid organisms

I am trying to self-learn some aspects of bioinformatics (coming from a stats background), and i am trying to find / download some VCF files for haploid organisms as an input to some statistical ...
user30279's user avatar
1 vote
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96 views

How to design a ChIP-exo experiment with controls?

Does anyone have any ideas on how to run a control/input sample for a ChIP-exo experiment? Is it even necessary to run a control (similar to input DNA for ChIP-seq)? I'm looking for any references ...
PaFi's user avatar
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173 views

Why do we use klenow fragment in pyrosequencing?

Why do we use klenow fragment in pyrosequencing instead of polymerase
roxaite's user avatar
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24 views

mtDNA sequencing error rates

What is the method to estimate the error rate in mtDNA sequencing? E.g. we are given a profile like this: 16069T 16126C 73G 152C Is there a method, a table of known values, or any other way to say ...
Andrea's user avatar
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182 views

How to construct tumor phylogenetic tree?

I would like to know if anyone has tried any software that constructs tumor evolution trees where the trunks represent the common mutations and the private alterations are noted on each branch. I can ...
civy's user avatar
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1 vote
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130 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 ...
Boris Burkov's user avatar
1 vote
0 answers
65 views

Walkthrough Illumina Genotyping

I would love help outlining a basic walkthrough of the wet-lab techniques for processing blood samples from patients, all the way to loading a BeadChip, to the part just before Next Generation ...
lrthistlethwaite's user avatar
1 vote
0 answers
381 views

How do we know Denisovans had 46 Chromosomes

What allows sequencers to conclude that Denisovans had 46 chromosomes rather than merely knowing Denisovans had the crossover material arranged in 48 or say 44 chromosomes? See http://genetics....
John Perkins's user avatar
1 vote
0 answers
633 views

Different names in paired-end sequence files

I am aligning paired end sequence reads using bwa mem and I get an error saying that ...
The Nightman's user avatar
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1 vote
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89 views

EMBOSS matcher and supermatcher - incongruent results?

I am trying to align a sequence to the mouse genome. I know a priori that part of my sequence should align to chromosome 9, but not all of it. I gathered that EMBOSS' ...
TheChymera's user avatar
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1 vote
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Superpatients for Cancer resistance

I was reading an article on MIT Technology review about superpatients for low cholesterol that got me thinking whether such patients exist for cancer. The article is http://www.technologyreview.com/...
user46725's user avatar
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What is the meaning of this poor sequencing result?

What is the meaning of this poor sequencing result? What is the problem? Can anyone guide me, please. Thank you.
Patomporn Phadungchaya's user avatar
1 vote
0 answers
156 views

What good is the MinION?

This year, Oxford Nanopore MinION has been shipped to some researchers for testing. The advantage of a table-top sequencer for diagnostics and personalized medicine is obvious. Similarly, research "...
Superbest's user avatar
  • 4,520
1 vote
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57 views

condensed protocol for sequencing a portion of human DNA from buccal sample

Anyone have a short & sweet protocol for PCR amplifying a region of human DNA (chromosomal or mt, I don't care) extracted from a buccal sample: including validated primer sequences and preferred ...
rhill45's user avatar
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1 vote
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what are hyperbranched amplicons in DNA sequencing?

I am reading an article about single-cell sequencing: http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2720.html And came across the concept of "hyperbranched amplicons". I googled for it but ...
719016's user avatar
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0 votes
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Identification of Secondary metabolites gene clusters in fungi

I am trying to identify secondary metabolites gene clusters specifically PKS from endophytes through PCR then sanger sequencing. Are there set of specific primers available or do I have to design my ...
Colyn's user avatar
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0 votes
0 answers
26 views

Is UMI necessary when analyzing samples from Formalin-Fixed Paraffin-Embedded tissues?

We have FFPE-tissues we would like to use for a sequencing run. we think we can get enough biological material, so the amount of RNA shouldn't be an issue, but we're not sure. A unique molecular ...
Assa Yeroslaviz's user avatar
0 votes
1 answer
61 views

Can contaminants in the DNA extract disturb the sequencing?

I'm having troubles with some DNA extractions. The yields are much lower than expected, and the Nanodrop spectrophotometer is showing quite a bit of contamination through the 260/230 ratios (see table ...
Joel's user avatar
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0 answers
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Sequencing a PCR product with no band

I did a PCR that successfully showed the appropriate bands one time, but when I tried to re-do the same PCR just at a larger quantity to send for Sanger sequencing, very faint or no bands were seen. ...
Nalonda's user avatar
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0 answers
44 views

How does one determine what sequencing coverage/depth to use?

In the context of rare diseases, what sequencing coverage will be sufficient to detect the mutated loci (for eg. SMN1, SMN2 CNVs, gene SNPS, INDELs etc) ? How does this relate to statistics and how ...
Loki123's user avatar
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