Questions tagged [sequencing]

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

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29 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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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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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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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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Why does the Wuhan coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)?

The Wuhan coronavirus's genome was released, and is now available on Genbank. Looking at it... ...
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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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81 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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252 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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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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366 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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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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51 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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83 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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70 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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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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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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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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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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50 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
56 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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243 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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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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165 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 ...
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227 views

Paired end sequencing with R1 and R2 of different length. Possible?

There are commercial sequencing kits/sequencers that allow for paired end sequencing in which the two reads obtained for each fragment are of different length? For example 150bp for R1 and 50bp for ...
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Produce a single sequential FASTA sequence out of BAM

I'm having problems properly looking for a solution because I'm a layman in Bioinformatics not familiar with the terminology. I'm hoping you can nudge me in the right direction, please! Thank you very ...
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72 views

Mixcr batch processing

I have a folder with 150 pairs of fastq files from an illumina sequence run. I need to precess them with mixcr, how can I do this in a batch with a single command?
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Crossover question from Coding Theory

I have a model that, for a given bit of code will produce a binary string. An example is given 01010101, it might produce {1,11}, and given 01010000, it may produce {2, 11}. I have a lot of these ...
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Genotyping technologies do not maintain phase?

Why exactly does genotyping not maintain phase? I guess I'm more confused on what's the difference between sequencing and genotyping, and as a result how phase is maintained in one, but not the other. ...
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85 views

Short reads vs long reads with regards to break points

My professor in class said the following statements. Short reads can map break points Long reads can disambiguate repeat related issues I'm very new to genomics, so I don't quite understand the ...
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116 views

Tools for quality trimming at 5 prime?

I'm looking for a tool that is capable to do quality trimming at 5' end and it is configurable. For example, I can choose the quality trheshold, the read length, etc. Any recommendations? I'm ...
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532 views

Significance and timing of “mux scans”

I'm using MinIONQC to do quality control on some ONT data. The software plots several read characteristics over time (hours passed during the sequencing process). These plots contain several vertical ...
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Are there any Genome in a Bottle-like resources for non-humans (especially for invertebrates)?

Genome in a Bottle is an excellent resource that provides many types of DNA and RNA sequencing reads for a single individual/cell line to test genome assembly and analysis tools. For example there are ...
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Separation of mixed plasmid DNA sequences post whole-plasmid sequencing

Imagine a DNA sample containing a mixture of different intact plasmids. These samples are sequenced using either MiSeq or HiSeq sequencing. Would it possible to assemble these plasmids post-sequencing ...
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113 views

Where to Download Cancer Raw Reads (fastq)?

Does anyone know where I can download cancer raw reads (fastq files), tumor and Germline for non-humans? I wanted to make a study with human data but I don't have the control access to download raw ...
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173 views

How to cluster the human genes by pathways/system-biology/metabolic properties?

I would like to make a chord plot from my data. I have a list of genes that according to my experiments are divided into 64 clusters of enrichment pattern. I would combine my 64 clusters with a ...
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423 views

Why do I get so many insertions from Minimap2 on my Nanopore WGS?

I'm a starting my analysis on nanopore whole genome sequencing. I start my analysis from this popular Github. The sample I downloaded was WGS for NA12878, so I would assume it's alignment to GRCh38 ...
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2answers
939 views

Hardware Requirements (specs) for Bioinformatics-dedicated desktop [closed]

I know this is a somewhat general or vague question, but I’m interested in your opinions. I must build a desktop for general bioinformatics activities with human genomes. I will work with Python and R ...
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How to score how densely bases are distributed along a given oligo?

Suppose I have a short chain string of oligos, and I want to rate them from 0 to 1 based on how clustered the "A"s are in respect to the chain. For example: ...
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559 views

Why does this human bam file only have one copy of each chromosome?

As we know that in human DNA sequence, one copy of chromosome comes from mother's DNA and another copy comes from father's DNA so as to form two copies of each chromosome in human DNA. So, if we ...
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477 views

Identifying Indels from Chromatograms

I have around 100 chromatograms (.ab1 files) from Sanger sequencing a genome at loci believed to have an indel. I'm new to interpreting this kind of data in ...
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Sequencing Deciduous Plants

Firstly, I'm personally not in the field of Bioinformatics, so apologies if this is a dumb question. Does anyone know of any research that has been carried out on the sequencing of deciduous plant ...
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Is there a read mapper that allows input in SAM format instead of FASTA/FASTQ?

When we get raw sequenced reads in FASTQ format, we usually need to do some pre-processing (QC, demultiplexing, etc.) prior to sequence alignment. The only way to register the results of this ...
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1answer
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E.coli Sequencing & Analysis

I have been given the task of assembling a 'new' Ecoli genome and analysing the genes present etc. The Ecoli is a new strain, and has been taken and run on a Nextseq 500 in high-output mode with ...
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345 views

What i5 index should I use on the Illumina sample sheet for an unindexed p5 primer?

I have an upcoming run on a HiSeq X and most of the libraries in the pool have both i5 and i7 indices. However, some of the libraries were made with the IS4 p5 oligo and it is unindexed. The IS4 ...
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713 views

Why are there more barcodes than GEMs in 10X chromium data?

Question: Why are there more barcodes than GEMs in 10X chromium data? Introduction I have several 10X genomics chromium libraries made with the de novo assembly/genome protocol. The 10X chromium ...
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What is the index fastq file (sample_I*.fastq.gz) generated when demultiplexing Illumina paired-end runs?

What is the index fastq file that comes with some Illumina sequencing datasets? (The samplename_I*.fastq.gz file.) For example, I recently received some 10X ...
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Extracting sequences from FASTA beginning with common 5' end

I am trying to figure out the best way to extract sequences from a FASTA file which begin with a common 5' region of 43 nucleotides. Preferably, I would like to to allow for "fuzziness" in this region ...
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dog coordinates (canFam3) to human coordinates (hg19)

I've converted dog coordinates to human using UCSC LiftOver. These are 200bp intergenic regions that are differentially methylated from normal dogs to cancer dogs. I've converted these to human ...