Questions tagged [sequencing]
DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule.
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1answer
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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
23 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
30 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
28 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 ...
4
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0answers
54 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 ...
-1
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1answer
54 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
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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
84 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
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2answers
59 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
25 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
84 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
56 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 ...
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2answers
88 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
53 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
votes
4answers
74 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
vote
2answers
78 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
vote
1answer
57 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
votes
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
votes
1answer
103 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.
...
1
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2answers
324 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
54 views
Overlap in Paired-end Reads for Sequencing?
Regarding Sequencing:
Do/can the paired-end reads have overlaps?
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2answers
149 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
50 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
vote
1answer
38 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 ...
1
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1answer
106 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 ...
1
vote
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
votes
1answer
60 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
178 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
262 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 ...
30
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5answers
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:
...
16
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1answer
1k 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 ...
10
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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
33 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 ...
161
votes
4answers
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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
159 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
118 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
270 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
vote
1answer
321 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 ...
8
votes
2answers
736 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 ...
1
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1answer
142 views
CRISPR/Cas9 screen analysis with Mageck: paired-end sequencing
I want to analyse data from a CRISPR/Cas9 screen (control vs. treatment) and I'm using Mageck (https://sourceforge.net/projects/mageck/). The problem is that I'm working with paired-end sequencing ...
2
votes
1answer
100 views
Sequencing center returns data in several files
We send some samples to sequence and we got several (fastq.gz) files for each sample. The files are distributed at two or three folders with different dates (more than a week apart). The dates of the ...
2
votes
1answer
177 views
Coverage required
I was came across a problem during an exercise in a book and I don't really know how to solve it. I feel like something's missing.
"coverage, c = $NL/G$ (N=number of reads, L=read length, G=genome ...
2
votes
2answers
81 views
How to best detect the “peaks” in RNA-seq data that are not assigned to any gene?
I encountered that many reads from single-cell RNA seq data were lost in the analysis because not assigned to any gene (genome: galgal6). I am trying to find an approach than could give me all the "...
1
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1answer
95 views
Plotting distance tree from blastn output
I'm trying to plot a simple distance tree of my blastn output with nj (like the tree view on NCBI). From what I understood, what I think I should do is
extract all the hsps from each alignment
re-...
1
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3answers
142 views
Python module for fetching NCBI id for a list of species
I have a list of scientific names of species. Is there a python module that can fetch NCBI taxonomy IDs?
3
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2answers
515 views
How to find common sequences among 6 multi-fasta files
I have 6 multi-fasta files, every of them contains ca 1500 sequences like that:
...
3
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0answers
106 views
High percentage of poly A sequences in 10X chromium R2 read
I'm currently analyzing two samples of eosinophil cells isolated from mouse lung and the samples are of very different quality.
According to the Cell Ranger summary 56% of the reads can be mapped to ...
