Questions tagged [sequencing]

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

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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 ...
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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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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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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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Find the date that sequencing was performed

I've got a bunch of RNAseq datasets from ENCODE and I'm looking to identify variables contributing to variance among my samples. For example, is there any easy way to find out the precise date which ...
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Which software is recommended for sequencing primers selection?

I have a list of primers for sequencing fungal ITS1/2 regions. I also have access to different fungal databases. I would like to perform in silico PCR analysis for comparing different primer pairs and ...
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I have two files: mys.nuc and ms.prep and need to use bioseq to extract the ORF sequences and save as “mys.nuc2”

Below are the two files I am working with: ...
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24 views

Drug-DNA complex simulation using AMBER

I want to carry out the simulation of drug-dna complex by placing the drug molecule at particular site in my DNA sequence (intercalating site). I have PDB files of both drug and DNA sequence. I will ...
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1answer
53 views

Shotgun analysis: Where and how to start?

I am a complete rookie in shotgun analysis, having only performed marker gene analysis before. I have a pipeline that I want to try but I can't wrap my head around how it all works. Please correct me ...
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42 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: ...
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71 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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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 ...
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74 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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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. ...