Questions tagged [sequencing]

DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule.

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22 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 ...
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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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1answer
32 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 ...
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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. ...
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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 ...
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2answers
60 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 ...
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33 views

marge 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 "/...
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1answer
54 views

Significance of k-mer length in COVID-19 sequence analysis?

I'm getting started in biology and bioinformatics with sequencing the SARS-Cov-2 or Coronavirus genome. I'm interested in this code which identifies k-mers in the genome: ...
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1answer
45 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 ...
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1answer
64 views

What is the meaning of these misaligned reads in a sequencing run?

I guess that's a basic question but I can't find an answer. I am analyzing some SARS-CoV-2 sequencing runs. I often find read alignments like the one in the image. ...
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2answers
128 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 ...
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43 views

Overlap in Paired-end Reads for Sequencing?

Regarding Sequencing: Do/can the paired-end reads have overlaps?
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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 ...
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47 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?
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1answer
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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
57 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
26 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 ...
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1answer
53 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 ...
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1answer
117 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 ...
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2answers
113 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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52 views

How can i get data set of illness and not illness people?

I'm new to bioinformatic .. i'm reading a paper and what i got that they made a classification for the people if they have a sequence of a disease or not ... ...
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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: ...
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1answer
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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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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 ...
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383 views

Using BaseRecalibrator in GATK4

GATK4's BaseRecalibrator uses a list of known variants to adjust the base quality scores in a BAM file. I would like to visualize the pre and post recalibration ...
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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 ...
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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... ...
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105 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 ...
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What kind of error-correction code is used in the error-correction code DNA sequencing?

In 2017, Chen et al reported a DNA sequencing technology called error-correction code (ECC) sequencing [1]. They borrowed ideas from communication and coding theory and encoded information redundency ...
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1answer
107 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 ...
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1answer
262 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
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170 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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517 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 ...
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2answers
188 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 ...
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How to confirming exon shuffling from genomic sequence, promoter sequence, and mRNA sequence?

I have the genomic sequence, promoter sequence, and mRNA sequence for a novel gene. It is thought that the gene is derived from exon shuffling of multiple genes. How do I characterize each of the 3 ...
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1answer
86 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 ...
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90 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 ...
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1answer
167 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 ...
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2answers
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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 "...
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1answer
90 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-...
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3answers
114 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?
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393 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: ...
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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 ...
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2answers
1k views

What is the name of this type of figure?

This figure comes from this wiki page. I googled "gene location figure" and "gene location plot", none gets similar results. I also tried search by image, none of the results is close. so, what is ...
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75 views

How to reproduce this specific sequence logo from 10 000 human mRNAs?

this is A sequence logo showing the most conserved bases around the initiation codon from 10000 human mRNAs. I would like to reproduce this sequence logo. How can I get the sequences? which database ...
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1answer
141 views

Is there a convention or standard of the highest bits in a sequence logo? [duplicate]

In bioinformatics, a sequence logo is a graphical representation of the sequence conservation of nucleotides (in a strand of DNA/RNA) or amino acids (in protein sequences). wiki says The total ...
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1answer
66 views

what does a sequence look like before alignment?

I am confused with Sequence alignment, which is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, ...
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1answer
589 views

How to compute the Shannon entropy for a strand of DNA?

I'm confused by the computation of sequence logo. Wikipedia gives a process about this without a concrete example. Let's just consider DNA, so there are 4 bases (nucleic acids). The following data ...
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1answer
135 views

Why do ten rows (Figure_1) correspond to 2 bits (Figure_2) in a sequence logo?

Following this question, I'm confused with the computation of sequence logo Following data comes from the book "Machine Learning - A Probabilistic Perspective (Figure_1)" here is the corresponding ...
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1answer
243 views

What is “aligned sequences” and “consensus sequence” in the context of sequence logo? How to compute these?

In bioinformatics, a sequence logo is a graphical representation of the sequence conservation of nucleotides (in a strand of DNA/RNA) or amino acids (in protein sequences). so, What is "aligned ...