Questions tagged [genome]

for questions related to whole genome analyses. For questions related to individual genes, use tag gene instead. Questions specific to format (like fasta) should be tagged with a format-specific tag.

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Is it possible to determine the genomic context of a gene in a Whole Genome Shotgun project?

After performing BLAST searches, I identified several genes of interest in a Whole Genome Shotgun (wgs) project. I know that gene X is located on scaffold 1234, from nucleotide 1 - 2250, while gene Y ...
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Coding object structure properties into a sequence

Hopefully, I found the right place to ask. Please, note that I'm not a specialist in the current field. Is there an algorithm to code information about object structural properties into a sequence (...
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Are the conclusions in “The proximal origin of SARS-CoV-2” legit?

I don't have any background in genetics and bioinformatics, so I ask you if you think that the arguments provided in the article The proximal origin of SARS-CoV-2 by Andersen et al. are convincing. In ...
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1answer
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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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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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8answers
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Since every human has a different DNA (different combinations of C, G, A, T) what does it mean to have the genome done? [closed]

I'm confused about the difference between genome and DNA. Is it correct to say that the same type of bacteria has the same DNA? But my understanding is that it is not correct to say that the same type ...
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1answer
28 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 ...
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1answer
27 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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0answers
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What Cellbase resources are 0-indexed, and which are 1-indexed?

The UCSC Genome Browser Team is clear about that the genome browser GUI is 1-based, closed interval. Genomic sequence retrieval via the UCSC REST API is 1-based, closed interval. All UCSC tables are 0-...
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1answer
63 views

Coronavirus phylogeny and evolution

This new article presents the phylogeny of the coronaviruses and the placement of the new coronavirus in it. This made me wonder of what we know about the coronavirus evolution, particularly where it ...
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0answers
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Do additional peaks in percent GC of PacBio gDNA reads indicate contamination?

I have two sets of PacBio reads from genomic DNA of an Aspergillus species that were made from separate preps of the culture. One of them has two additional peaks at 38% and 60% in the percent GC ...
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1answer
45 views

efetch nucleotide -> protein ids

I'm downloading translated viral genomes initially via Blast - which had shortcomings - and now by efetch. What I want to do is obtain a complete list of all ...
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1answer
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Looking for a tool to find 16S rRNA in hundreds of genomes

I have hundreds of bacterial genomes and I would like to know which is the best informatic tool in which I can run all genomes on one go and get a 16S rRNA gene sequence of each genome as output. ...
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How to calculate coverage depth of genes in an annotated sequence?

I have a metagenomic dataset across multiple samples that has been grouped and binned (we did this due to poor sequence quallity). I have annotated the bins and now want to calculate the abundance of ...
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1answer
87 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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28 views

How to check the distribution of gene expression across the genome?

I have a group of genes with the same functionality belonging to 3 different families. I would like to see how their expression is distributed across the genome: do they tend to be expressed in a kind ...
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1answer
26 views

Use of Electronic Phenotype in EHR

May I know what's the use of Electronic Phenotyping using EHR data? I did refer this link but have few questions I understand that ...
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2answers
76 views

Is there any way to align ChIP-seq reads to telomeres?

I know that telomeres are highly repeated sequences, but is there any way to retain any reads that map to these regions (on HG38)? I recently managed to find some protein binding to centromeres, ...
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2answers
72 views

Determining the quality of a publicly available genome assembly

I am looking for homologous genes in various protozoan species using BLAST. The genome sequences of these species are deposited in NCBI's WGS database. NCBI’s webpage includes the global statistics ...
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1answer
86 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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1answer
168 views

How can I locate duplicated regions in a sequence?

I am facing an issue when trying to align short reads against a region in human chr5. The two Sensory Motor Neuron genes, (SMN1 and SMN2) are almost 100% identical and this causes the aligner to fail ...
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1answer
36 views

How to output only the overlapping region of two files?

I have two files of genomic coordinates. I am trying to output only the overlapping region of fileA if it intersects with fileB. Not the original fileA coordinates. fileA ...
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5answers
427 views

Is the genome a programming language (i.e. LISP)? Can we analyze it with computer science theory?

Question moved here from the biology stack exchange. It looks like the genome is a kind of LISP language. Operon structure of genome: - https://github.com/philschatz/microbiology-book/blob/master/...
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1answer
42 views

How can I predict if the binding site of a DNA-binding protein is located on the promoter sequence of a gene?

Is there any computational tool or any other method to predict if the binding site of DNA binding protein is actually located on a promoter sequence?
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1answer
40 views

Genome annotation of a Bacillus strain

I finished the sequencing of the genome of a biocontrol activity strain Bacillus amyloliquefaciens by Illumina hiseq. I have already gone through some papers but there were no details of processing in ...
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1answer
187 views

Consensus sequence from SAM or BAM file?

I am trying to perform reference-based assembly. Most of the tutorials teach how to create a bam file and view alignemnts in IGV or Tablet. But, I want a assembled genome sequence in fasta format. How ...
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1answer
51 views

Viral genome finishing

I have assembled poxvirus genome using Ray. The assembly is good. Out of several thousand contigs I got, I was able to get one scaffold using Contiguator tool, which is about 90% of my genome. I have ...
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1answer
47 views

Viral genome assembly using broad viral ngs pipeline?

I am trying to assemble RNA virus genome using Broad Viral NGS pipeline BROAD VIRAL NGS PIPELINE. I am two questions : 1) As this pipeline requires unaligned bam format as input, how do I convert ...
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What does this genome file from NCBI means? [closed]

I obtained a genome from NCBI. For instance, Haloquadratum walsbyi strain AM180088.1. But the FASTA file contain two parts. The first part marked as >AM180088.1 Haloquadratum walsbyi DSM 16790 ...
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2answers
192 views

mapping heteryzygous kmers on a genome

I have a set (a couple of millions) of kmer pairs of known length (usually 21) that I know that are heterozygous in the middle nucleotide. For instance: ...
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1answer
105 views

Pipeline for extracting gene from multiple genomes for use in HyPhy selection analyses?

I have been trying to obtain some preliminary data from HyPhy selection analyses to inform a larger project. I have obtained a number of assembled mammalian genomes from NCBI with the initial goal of ...
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1answer
29 views

Is there a resource where I can donwload E. coli assemblies grouped by their pathotypes?

I will preface this by saying I'm not a microbiologist, so I apologise for any haziness and I'll be happy to expand. I would like to download the assemblies of different E. coli genomes and group ...
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2answers
241 views

Unable to install bedtools on windows 10 ubuntu

I am trying to install bedtools on windows 10, but I get an error I don't understand. How can I fix it? ...
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4answers
378 views

Identify non-coding regions from a genome annotation

I have this GTF file and I use the command below on a Linux machine to extract the coding regions of the genome: ...
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233 views

wtdbg2: practical implications of k-mer fsize and psize choice

I am using wtdbg2 2.3 to assemble a human genome (sequenced on PromethION from a cell line). I filtered out reads with low average quality, and now I am trying to determine the parameters that will ...
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1answer
63 views

Seeking explanation of the hg38 files downloaded from bowtie 2 website

I downloaded the H. sapiens, NCBI GRCh38 files from Bowtie's website. After unzipping, there are 6 files, 4 that end in set 1.ebwt, set2.ebwt, set3.ebwt, and set4.ebwt and two that end in set.rev.1....
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1answer
81 views

Prediction of prokaryotic origins of replication (ORI)

I want to predict origins of replication (ORI) on hundreds of prokaryotic genomes. The most straight-forward solution would be to use most commonly used tool, Ori-Finder. It uses integrated gene ...
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1answer
163 views

How to plot genomic.fna fasta file in R using Gviz?

I downloaded the genome of Staph aureus as DNA sequence from NCBI. I would like to visualize it using Gviz. Is Gviz the right tool to visualize genomes? What are the necessary steps from the sequence ...
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6answers
535 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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1answer
357 views

How can I identify a recessive and dominant gene?

For example, I have two allelic genes. How can I identify a recessive and dominant gene? Are there any databases with this information? Or the answer to my question is to study the concept of "...
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1answer
74 views

Simulate and test CNV workflow?

I'd like to evaluate a CNV project. My aim is to evaluate if the scripts are sufficient for calling reasonable CNVs. I know they have a paper, but their scripts may be buggy... and all papers are ...
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2answers
327 views

full visualisation of draft genomes alignment

I have two draft genomes (aprox. 500Mb each), one with ~10'000 scaffolds (genome1.fasta) and one with ~1'000 contigs (...
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1answer
133 views

Tool to show DNA sequence and allowing upload of own graph data

Background We want to be able to load (or request) data for a genome including the sequence and gene annotation (bacteria). Then, we want to load our own annotation which should be displayed as a ...
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Finding gene name from human genome using SP1 transcrition factor binding site from Postion Weight Matrix

I have a list binding site motif of SP1 transcription factor which collects from PWMScan tools. Actually this tool scan whole human genome and give the entire binding motif list. From that list of ...
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2answers
39 views

How to generate Genbank format out of paired end fastq data?

I've unmapped cleaned paired end sequence data in fastq format of a bacterial genome. I want to get a sequence data in Genbank format in the end. What are the exact steps that I have to follow in ...
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2answers
530 views

Python API for working with ENSEMBL genomes

Dear bioinformaticians, I could find two python APIs to mine ENSEMBL genome databases. There is a pyensembl which is more popular and then there is ...
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1answer
126 views

How to assess the quality of assembled .fasta genome files?

I have assembled 3 .fasta files from contigs infastq format of 3 different Homo sapiens. I would like to see if the assembled ...
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1answer
356 views

STAR Indexing Diference for Small and Large Genome File Output

I have a quick doubt on the output of the Genome Indexing, I have used the STAR program along with genome .fasta file and GFF file. Genome size is 3GB, here is the file output ...
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808 views

estimate genome size: kmer-based approach from PacBio reads

Can anyone suggest a software/method for kmer analysis using PacBio reads (RSII)? Something similar to Jellyfish, that I saw in a nice tutorial - but must be suitable for long, noisy reads. ...
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0answers
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How to visualize genome track of gene in specific cell-lines?

I'm trying to make a plot showing genome tracks of specific genes in specific cell-lines of RNA-seq and Chip-seq data. It should look something like this I have recently seen this encode, but in ...