Questions tagged [genome-sequencing]
The genome-sequencing tag has no usage guidance.
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How to identify phages from Phaster in PhageDB
I am running searches for genes using Phaster {PHASTER (PHAge Search Tool Enhanced Release) is a significant upgrade to the popular PHAST web server for the rapid identification and annotation of ...
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How to interpret a GenomeScope plot?
I am working on a new sponge genome and I have produced the genomescope plot from the 21-mer kmer frequencies. I have hard time interpreting the plot. Can someone please help me?
Thank you.
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Can someone help me estimating the runtime of the pipeline applied by the vertebrate genome project?
The vertebrate genome project (VGP)
has a lot of interesting publications such as this one.
The rough pipeline is outlined below:
Here the pipeline in more detail:
While the paper describes all the ...
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Locate the saved template of minknow
I am using minknow on ubuntu. After saving the template (settings), where is that file locally stored in the system?
Also what is its format/extension?
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Genome assembly of SRR12196449 with SPAdes
I am trying to assemble the run SRR12196449 with SPAdes. The description of their project is:
This project expected to standardize a method for amplification and
...
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Is this a complete bacterial genome? (CheckM)
I've been working with a bacterial genome assembly. The initial stats look pretty good (3 main pieces, depth ~50x [20x - 100x] if I calculated it right). I'd expect this to be a virtually complete ...
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Pros and cons between genomes and transcriptomes?
What are the major differences between the use cases of a shot-gun genome and an mRNA capture transcriptome? Especially when it comes to downstream analyses such as looking for orthology, and ...
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Length of Contigs in Transcriptome and Whole Genome Assembly
Why are there shorter contigs from transcriptome assembly than from a whole genome assembly? I know the difference between transcriptome and genome, but don't really understand what contigs are in the ...
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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 ...
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Which one is a more convenient assembly?
I have developed a software for de novo genome assembly. Its performance varies gradually according to how much data you employ. At initial stages it often produces contigs that look like that when ...
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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 ...
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Publicly available genome sequence database for viruses?
As a small introductory project, I want to compare genome sequences of different strains of influenza virus.
What are the publicly available databases of influenza virus gene/genome sequences?
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Extract reads from bam files by their @RG
How could I extract reads from bam files by their read groups @RG ?, I've got one file containing all reads for 5 samples, the SM is appears NONE, So, I want to extract each sample reads by the @RG ...
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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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Overlap in Paired-end Reads for Sequencing?
Regarding Sequencing:
Do/can the paired-end reads have overlaps?
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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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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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Tools for simulating Oxford Nanopore reads
Are there any free open source software tools available for simulating Oxford Nanopore reads?
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How do researchers account for heterozygosity in genome assembly?
this is a very general question about diploid genome assembly. I am wondering how people deal with heterozygous region in a genome when assembling ?
Do they pick one of the haplotype to be in the ...
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What are 2D reads in the Oxford MinIon?
Reading the Mash: fast genome and metagenome distance estimation paper, I see the reference to "2d reads" notion under the minION context (a sequencing technique)
e.g
...
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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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What are the pros and cons of the different basecallers in Oxford Nanopore Technology Sequencing?
What are the pros and cons of the different basecallers in Oxford Nanopore Technology Sequencing?
I am about to start a MinION run on my laptop. What should I consider when choosing my basecaller? ...
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Generating basic dna sequences in R
Looking for some guidance.
In an introductory bioinformatics class I am tasked with doing the following in R:
Create the sequence ACTGACTG
Generate a random string of nucleotides with equal ...
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Genotyping with Illumina HumanOmni1-Quad before whole genome sequencing
I read a paper about (whole genome sequencing analysis of 100 Southeast Asian Malays. It says "Prior to library preparation, each sample was genotyped on the Illumina HumanOmni1-Quad as an initial ...
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Can I run STAR without an annotation file?
I wish to use Rascaf to scaffold a fragmented draft genome.
For this, I need to provide a BAM file of aligned RNA-seq reads and the draft genome.
So, I indexed the draft genome with STAR like this:
<...
CommunityBot
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How to QC overamplified shotgun library?
I made some NEB ultra II whole-genome shotgun libraries with around ~200ng of template going into the indexing PCR step. The PCR was run for 13 cycles and I ended up having high library concentrations ...
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Can the canu assembler output a fastq file of the final assembly just like HGAP4?
I have assembled some genome from Sequel PacBio data both with HGAP4 on the SMRT Link interface and using canu on the command line. The HGAP4 assembler outputs a fastq file of the final assembly such ...
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How do PCR duplicates arise and why is it important to remove them for NGS analysis?
I am trying to understand PCR duplicates in NGS analyses (actually whole-genome). I searched, and the best answer I found is in this blog.
However I don't understand if I understood how PCR ...
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Downloading a reference Genome for Bowtie2
How do I download a reference genome that I can use with bowtie2? Specifically HG19. On UCSC there are a lot of file options.
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