Questions tagged [sequencing]
DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule.
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questions
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1answer
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Low pass sequencing has been reported to detect common variants. How low can one go and get reliable data? Is 2X pass sequencing analysis possible?
I would like to use low pass sequencing to replace a genotyping chip to be able to detect variants up to 0.1 % allele frequency in available population data. What is the minimum depth I can opt for to ...
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0answers
68 views
Illumina vs PacBio vs Nanopore price
Can someone help me with comparing the cost per run of Illumina, PacBio and Nanopore sequencing technologies?
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1answer
32 views
Which format is the most raw format
I wanted information regarding which format is considered the most raw from an illumina sequencer ?
fasta
fastq
bcl
bam
As per my research it should be bcl but I am not sure.
0
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1answer
44 views
Which sequencing technologies are considered short read
I couldn't find any information on this online. Which of the following sequencing technologies are considered short read technologies? Illumina, Oxford Nanopore, Ion Torrent, Pacific Biosciences
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2answers
64 views
Construct the Overlap Graph of a Collection of k-mers
I am doing a course on graph algorithms in genome sequencing and the current assignment involves building an overlap graph from a bunch of k-mers. Formally the problem is as follows:
Input: A ...
2
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1answer
56 views
What is the right way of calculating a Phred score by hand?
i am trying to calculate mean Phred scores for my sequencing data, but i feel not very comfortable about it. There are actually two ways of calculating. (I just use an existing sample)
giving: 3 reads ...
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2answers
64 views
Get frequency of index sequences of fastq file
I recently did some sequencing on a MiniSeq and unexpectedly the Undetermined_S0_L001_R1_001.fastq.gz file contained quite a lot of data (about 40% of total). I ...
0
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1answer
19 views
Modeling number of reads mapped to a gene
I am looking for a probability distribution of a number of reads mapped to a particular gene in metagenomic sequencing (NGS, shotgun, likely illumina).
Naively one could model it via a binomial (or ...
-1
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2answers
65 views
Filter rows of VCF file for Match=EXACT?
How do I remove rows in a VCF file on 1kGenome column, where Match=EXACT using bash ?
0
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1answer
27 views
What is a PacBio “movie file”?
I came across references to "movie files" from PacBio sequencing in this paper:
https://www.jimmunol.org/content/204/12/3434
Specifically:
Movie files used to generate results presented in ...
0
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1answer
38 views
How to determine a correct promotor sequence? (Bisulfite sequencing - uni assingment)
aspiring bioinformatician here, I'd like to ask you for help with an university assignment. First let me post the entire question:
...
0
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1answer
31 views
Quast duplication ratio and mismatches percent
When analyzing Quast results it seems that it doesn't calculate mismatches and indels in a useful way if the "Duplication ratio" is over 1.
For example, that's what I get for an assembly ...
6
votes
1answer
64 views
How to search for high coverage SRA entries
The Question
I want to find high coverage SRA entries, e.g., above 100x.
I guess the best way is to use https://www.ncbi.nlm.nih.gov/sra with an appropriate search term. I don't mind if the search ...
0
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1answer
64 views
Metagenome simulation from a concatenated FASTA file
I am trying to simulate metagenome sequencing. So I will start with a file with a lot of concatenated genomes. From there, I would like to randomly extract 10,000 sequences of length 200bps.
I got ...
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1answer
20 views
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0answers
23 views
DNA sequence error annotation
Suppose I generate a DNA sequence of the following pattern.
AAGTC
And after being passed through a channel with insertion, deletion and substitution errors obtain the following sequence
AAAGGC
Where ...
2
votes
2answers
91 views
How can I subset WGS data to the level of WES variants?
I would like to compare mutational signatures1 in patients from different studies, however some studies are based on exome seq (i.e. ~20,000 coding variants) and some are from whole genome seq (i.e. ~...
2
votes
2answers
73 views
Are sequencing reads written differently when inserts and indexes are sequenced seperately?
I was going over different sequencing library protocols and noticed that the adapter sequence can vary between protocols. In some adapter sequences the index sits between the primer binding site and ...
1
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0answers
26 views
Fastq dataset after clustering
I'm doing a project for DNA archival storage systems
Is there an open-source dataset used as ground truth for clustering?
E.g
A file containing the ground truth strand sequences, which have been ...
3
votes
2answers
85 views
Virus genome: protein inside another protein
The genome sequence for the GenBank virus JX869059.2 (a human betacoronavirus) contains, among others, two proteins:
N protein (range 28566..29807) and
Orf8b (range 28762..29100).
The interval for ...
0
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0answers
61 views
Resources to learn genome assembly workflow for small genomes (like viruses)
I have sequencing data of a few samples of a DNA genome virus. I'd like to learn de novo assembly of the ...
1
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2answers
89 views
Bacterial DNA at the tail of transcriptome reads. What does that mean?
I am assembling a transcriptome obtained from the Internet. The transcriptome was extracted from a human cancer tissue that had been previously grafted into a mouse. I have detected that many ...
0
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1answer
67 views
How to anonymise a bam file
I have a bam file of, for instance, RNA-Seq, which contains patient-identifiable data in the form of Single Nucleotide Polymorphisms (SNPs) throughout.
I would like a technique to take this aligned ...
0
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0answers
34 views
How many markers or loci are used in forensic DNA profiling and the effect of the DNA sequencing?
I am reading the Wikipedia page on DNA profiling, specifically the STR analysis. It says the DNA profiling relies on 20 or so loci matching. It also gives an account of finding false identification. ...
2
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4answers
82 views
Separate multiple sequence into different file, one sequence per file
I have a file contain multiple sequence, and I want to separate them by "gene:" into different file.
example:
example.fa
...
1
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2answers
95 views
How to combine two Genome-wide Association Study (GWAS)? [closed]
I did a GWAS analysis in the past for antibiotic resistance of E. Coli and the results were interesting (matching the literature). I did a new GWAS analysis for some new samples, but the results are ...
1
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1answer
63 views
merge the matrix from computematrix of deeptools
I have several matrix from computematrix of deeptools. I need to merge two of them using "computeMatrixOperations cbind -m input1.mat.gz input2.mat.gz -o output.mat.gz"
but I am running to error "/...
2
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1answer
56 views
Assembly reads having a copy of their beginning in their tail
I am analyzing the reads for the SARS-CoV-2 assembly with id SRR11140748. Apparently these reads were obtained with parallel sequencing by Illumina and Oxford Nanopore Technologies.
I have found these ...
2
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1answer
112 views
What is the meaning of these misaligned reads in a sequencing run?
I am analyzing some SARS-CoV-2 sequencing runs abd often find read alignments like the one in the image.
...
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2answers
435 views
Marking optical or PCR duplicates with picard vs. samtools flagstat
I am trying to identify the best library prep method for noninvasive prenatal test samples, to be sequenced with Illumina Novaseq.
One metric that I am evaluating is the number/ percentage of PCR or ...
3
votes
1answer
65 views
Overlap in Paired-end Reads for Sequencing?
Regarding Sequencing:
Do/can the paired-end reads have overlaps?
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2answers
154 views
Can I automate CLUSTALO and output alignment sequence identity?
I've detected homology between targets of ligands in drugbank and proteins in the proteome of a pathogen. I've parsed the output very rudimentary and calculated my query coverage. This exists in an ...
1
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1answer
52 views
Location of Reads in Sequencing
I have questions regarding sequencing:
Are paired-end reads from different stands?
What about single reads, are they coming from both strands?
1
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1answer
41 views
Warning in fastqc
I am checking the quality control of my sequences using the Fastqc tool. For some steps, like "Per base GC content", etc., I received a warning. So, I was wondering whether I Should also take care of ...
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1answer
123 views
Per Base Sequence Content in fastqc
I have a question regarding "Per Base Sequence Content" plot for "fastqc":
In the fastqc documentation, it is written: "In a random library you would expect that there would be little to no ...
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1answer
27 views
Cutting the sequence into several sequences with the information of a dataframe
I have a fasta file with several 120-concatenation protein sequences. I also have a data frame with 120 names of proteins in column 1 and their length in column 2. Using this dataframe I want to ...
2
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1answer
63 views
Translating a genome sequence into possible frames
I have a sequence below from MYC gene about which I need to translate the sequence in all possible frames AND identify (for each frame) which codons are actually used in MYC
...
0
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1answer
215 views
What samples can be used for a Mutect2 Panel of Normals
I'm working on calling somatic variants from solid tissue tumors. I have one normal and one tumor sample for each patient. I plan to use Mutect2 to call somatic variants after preprocessing the data ...
2
votes
2answers
363 views
Importance of Proper Pairs vs Aligned Reads for RNASeq data
I have stranded, paired end RNASeq reads that I have aligned using STAR. I plan do conduct a differential expression analysis with DESeq2. After running quality control checks, a good portion of my ...
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4answers
8k views
Why does the FASTA sequence for coronavirus look like DNA, not RNA?
I'm looking at a genome sequence for 2019-nCoV on NCBI. The FASTA sequence looks like this:
...
18
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1answer
2k views
Is it possible for coronavirus or SARS to be synthetic?
I have heard several conspiracy theories regarding the origin of the new coronavirus, 2019-nCov. For example that the virus and/or SARS were produced in a laboratory or were some variant of Middle ...
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3answers
2k views
A new paper suggests the Corona Virus has “Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1” - What does this mean?
Quote:
We found 4 insertions in the spike glycoprotein (S) which are unique to the 2019-nCoV and are not present in other coronaviruses. Importantly, amino acid residues in all the 4 inserts have ...
0
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1answer
34 views
probability of an entire sequence, not just one value
I am reading "Statistical methods in bioinformatics"
I came across this formula:
As explained in the book O are the observations:
My question is why the author ...
164
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4answers
88k views
Why does the SARS-Cov2 coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)?
The SARS-Cov2 coronavirus's genome was released, and is now available on Genbank. Looking at it...
...
0
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1answer
190 views
Interpreting MultiQC plot of GATK BaseRecalibration data?
I'm using GATK4 to build a somatic variant calling pipeline. The pipeline uses MultiQC to aggregate quality control data, and one of the QC measures reported is base quality score recalibration from ...
2
votes
1answer
121 views
Any user friendly way to find rare mutations in whole genome raw?
Is there any user friendly way to find rare mutations in the individual human whole genome sequencing raw data? (from Dante, 30x coverage).
To be more specific, I want to find mutations from this ...
2
votes
1answer
276 views
Why don't all reads have adaptors?
I got NGS reads back from sequencing platform. I check for adaptors and trimmed them. But I realized only a fraction (eg 30%) have adaptors... why not all of them?
Thanks
1
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1answer
423 views
Low Fraction of usable antibody reads in CiteSeq
we performed a combined gene expression and CiteSeq experiment with the 10x VDJ kit and 20 conjugated antibodies and sequenced on hiseq. I used cellranger to process the sequencing output. The ...
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votes
2answers
894 views
What is 'k' in sequencing?
When a DNA sequence is sequenced, I've only ever dealt with A,T,C,G and N which indicates un-identifiable bases. However, I came across a 'k' recently and I had asked another researcher who gave me an ...
2
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2answers
1k views
What is a read count?
A very basic question: What exactly is a read count in shotgun sequencing and how is it calculated? I'm particularly interested in understanding the definition of the read count in the context of ...
