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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1answer
29 views

How to fix RepeatMasker.lib.nsq missing error when running RepeatModelor?

I have run RepeatModelor and I don't see the classified output file. I got this error. ...
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Why I get Singularity error when I try to run MAKER Genome Annotation on HPC?

I need to run MAKER genome annotation for my assembly file on HPC and I'm new to this. When I try to do that I get this error. ...
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1answer
42 views

Truble to run a multiprocessing kmer count script

Hi there I have this code: ...
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1answer
45 views

How can I get or create a reference genome for Bacteria?

I am a computer engineer and nowadays trying to grasp some concepts of Bioinformatics particularly, reference genomes and genomic variants. My aim is to find the effect of sequence features on variant ...
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34 views

Which of the Transcriptome assembly method is best for identifying novel lncRNAs?

I'm working with human samples and I'm trying to identify novel lncRNAs from tumor samples of Prostate cancer. I'm using reference based transcriptome assembly with ...
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46 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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8 views

How do I include repeat purity, default slippage, default stutter, and minimum flanking (left and right) in Tandem Repeat Finder's output?

I am attempting to create a markerInfoFile for use in a program called popSTR (GitHub Documentation: https://github.com/DecodeGenetics/popSTR). The marker info file should contain information about ...
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1answer
253 views

Samtools Index: Chromosome Blocks not Continuous

I am working with short-read whole-genome sequences from the NCBI's SRA. I have aligned and sorted all of my short-read sequences and am attempting to index each sequence into .bai format using ...
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1answer
31 views

Seurat DE t.test

I am new to the Seurat package and was looking at the tutorials on the Seurat website and am just curious to know if there is any way to perform a t.test for the expression of a specific gene between ...
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15 views

Select for a specific proportion of a genomic feature

Currently have a bed file with exon coordinates for a list of about 20 genes, and I want to select the exons that fall within the first 3/4 or 2/3 of the coding region for each gene. Does anyone know ...
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33 views

Coding vs non-coding DNA length

I am trying to calculate the total exonic length (in bp) in order to see where the coding-noncoding ratio of roughly 1% to 99% comes from. We know all chromosomes total about 3 billion base pairs. So ...
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What is the origin of the 'source Gene ID' references given in the 'gene_presence_absence.csv' output of Roary?

I am learning to use Roary for preparing a pan genome for some lactobacillus strains. In the 'gene_presence_absence.csv' output of Roary (which i view in excel), a 'source Gene ID' is given for each ...
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1answer
37 views

BWA: Detecting Variation between Reference Genome and Short-Read Sequences

I need to identify all loci in the short-read sequence at which the number of microsatellite repeats (i.e. number of copies of "AA," "GTC," etc.) differ from the reference genome, ...
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1answer
26 views

How to use the DI-tector software for defective genomes analysis?

I am trying to use a free .py script from this site http://www.di-tector.cyame.eu/ while unfortunately there's neither manual nor any documentation presented. ...
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1answer
32 views

How can I convert codon coordinates to genomic position?

I am looking for a given mutation in IGV, which accepts coordinates in the form of chr<X>:<Y> Where X is the chromosome number and Y is the base ...
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1answer
20 views

Get a single number representing the contact probability between a pair of genomic loci using HiC data

Hello to the experts in analyzing chromosome structure data in HiC format, I have a very basic question. I have a HiC file (specifics are mentioned below), using which I would like to obtain contact ...
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What does it mean if aligned genomes are not of the same length?

I am aligning 4 genomes of Psuedomonas chlororaphis using progressive mauve software. Command used: ...
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24 views

Finding regions between ORFs

I'm doing work on mRNA and need to get predicted mRNA sequences from a genome. I'm working with this genome https://www.ncbi.nlm.nih.gov/nuccore/U00096.3 (E. coli k-12 mg1655). So have a genome ...
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2answers
63 views

how to use list of gene id to get cds sequence(cds fasta file have many annotation, only gene id: is same to query id)

i have a question when i want to extract cds sequence using gene id. but cds file is not just start with >gene is, it has many other annotation. the only same is star with gene: cds fasta: ...
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2answers
429 views

BERT Language Model and Gene Sequences - How Do I Relate Clusters of Sequences?

I hope you'll indulge a question from a computer scientist with limited bioinformatics knowledge. I've been working with the Google tool for language modeling called BERT. It's generally regarded ...
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1answer
24 views

How can I find the position of every mutation where the Allele Frequency is greater than X, in regards to a reference such as Hg19?

I have a Human genome sequenced in a BAM file (along with other files with the indels, snps, cnvs). I want to find every mutation with regards to the reference Human genome. However the majority of "...
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1answer
69 views

Getting sequences of one transcript per gene out of annotation and genome

I got a genome (data/genome/genome.fasta) and braker-based genome annotation (data/genome/annotation.gff3), now I would like to ...
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2answers
935 views

How can I classify the 3 clades(S, G, V) of the coronavirus without using protein data?

On GISAID they classified the coronavirus using 4 clades(S, G, V, Other). I downloaded around 1,000 complete genomes of the coronavirus from GISAID and I would like to classify each one as belonging ...
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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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24 views

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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1answer
336 views

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
43 views

Overlap in Paired-end Reads for Sequencing?

Regarding Sequencing: Do/can the paired-end reads have overlaps?
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1answer
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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8answers
4k views

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
37 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
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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0answers
20 views

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
79 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
23 views

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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2answers
57 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
33 views

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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0answers
37 views

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 ...
2
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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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0answers
29 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
54 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
79 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
159 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
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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1answer
273 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
67 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
491 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
43 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
66 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 ...
2
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1answer
248 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
60 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 ...