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.
173
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Uppercase vs lowercase letters in reference genome
I am using a reference genome for mm10 mouse downloaded from NCBI, and would like to understand in greater detail the difference between lowercase and uppercase letters, which make up roughly equal ...
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Why sequence the human genome at 30x coverage?
A bit of a historical question on a number, 30 times coverage, that's become so familiar in the field: why do we sequence the human genome at 30x coverage?
My question has two parts:
Who came up ...
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What Ensembl genome version should I use for alignments? (e.g. toplevel.fa vs. primary_assembly.fa)
When you look at all the genome files available from Ensembl. You are presented with a bunch of options. Which one is the best to use/download?
You have a combination of choices.
First part options:
...
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8
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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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Improve a reference genome with sequencing data
I have a DNA sample which I know doesn't quite match my reference genome - my culture comes from a subpopulation which has undergone significant mutation since the reference was created.
The example I ...
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9
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2
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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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3
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How to calculate the memory usage of storing kmers in RAM
I want to write a program in C++ that stores kmers in a hash or in a trie. How can I calculate how much RAM I would need for each type of data structure? For this application my kmers are strand-...
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Aligning many long sequences
I'm faced with having to align many (some 100s) bacterial genomes, where the genome length is in the millions. Obviously, this is beyond normal alignment techniques and it's unclear to me what the ...
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How should the popular press compare similarity of genomes?
Note this is a question from a lay reader.
I've read in the popular press that ~1-4% of the genome of non-African Homo sapiens is inherited from Neanderthals, or that Melanesians derive a similar ...
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How to use Python to count k-mers?
I have some FASTQ sequence files and a FASTA file for some regions I'm interested in.
I would like:
Build an index for the FASTA file
Use the index to count number of k-mers occurred in my sequence ...
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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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8
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2
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Comparing two genome annotations
I have one-dimentional array (human genome). Also I have two annotations for it, we can think about them as different peaks (it's nucleosome and secondary structures). How can we find correlation and/...
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bed file with N regions of GRCh38 reference?
How do I obtain a bed file with the list of N-regions of GRCh38 reference? This is, the regions where the sequence is a stretch of Ns.
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Is this a low complexity region in our human genome?
I have a screenshot where many of my reads were aligned to a region that I suspect a low complexity region. Although you can't see, all those reads are clipped in the cigar strings. Sample cigar ...
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dividing genome into non-overlapping windows using R
I have nearly 10 million SNPs located on 10 chromosomes. I want to divide the genome into non-overlapping windows of 15, 20 and 30 kb. Here is part of my SNP table:
...
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7
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1
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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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1
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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:
...
6
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2
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What is indel calling and what is its purpose?
I'm having a difficulty in grasping the general purpose and concept of indel calling.
What exactly is this process?
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5
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What is the standard way to work with a diploid reference genome? Complementary strands?
At the moment, the standard reference genomes (e.g. hg19, hg38) are haploid genomes. We know that the human genome is diploid. Naturally, the latter would be the respectively correct representation of ...
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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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1
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Does the DNA or RNA of some ethnic groups map better than others' to the human reference genome sequence?
I believe that the human genome reference took DNA samples from different people and that some natural variation is included in extra contigs.
However, the human reference genome comes from a ...
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6
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1
answer
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How to efficiently compute the exact percentage of non-unique k-mers in a genome for given k?
I'm looking for some software that can "efficiently" (time and memory) compute the exact percentage of non-unique k-mers in a genome for given k. I don't need the k-mers or the abundances itself, I ...
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Is it wise to use RepeatMasker on prokaryotes?
I'm looking for a way to identify low complexity regions and other repeats in the genome of Escherichia coli. I found that RepeatMasker may be used for example when drafting genomes of prokaryotes (E. ...
6
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2
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What tools can I use for a bacterial core/pan genome pipeline?
I want to perform a genome comparison on a group of isolates. I want to look into two broad groups of taxa and compare the accessory genome in each group. I have been using prokka (v1.12) and roary (...
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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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2
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183
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Genome assembly from error-prone reads
I understand how to assemble genome from error-free reads. I implemented like this:
Construct directed overlap graph with reads as vertices and edges as
maximum overlap between two vertices. ...
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2
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What is the difference between a transcriptome and a genome? [closed]
I have a computer engineering background, not biology.
I started working on a bioinformatics project recently, which involves de-novo assembly. I came to know the terms ...
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1
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Why does the SARS-Cov2 genome has letter t [duplicate]
ATTAAAGGTT TATACCTTCC CAGGTAACAA ACCAACCAAC TTTCGAT... is part of the 5'UTR of genome of an RNA virus SARS-Cov-2.
RNA contains letters ...
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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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Way to get genomic sequences at given coordinates without downloading fasta files of whole chromosomes/genomes first?
So I have a list of start and stop positions along chromosomes in different species, and I'd like to get the corresponding DNA sequence for each set of coordinates. In the past, I've just download the ...
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2
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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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1
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Can I index a compressed FASTA file using STAR?
I am using STAR to align RNA-seq reads to a reference genome. Before the alignment, I need to generate an index of the reference genome. I use the following code to generate the index successfully:
<...
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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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Simplest way to work out structural variant type?
In VCF 4.2, a structural variant (SV) can be described with the BND keyword in SVTYPE. For example, the following example is an ...
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Find paralogs in a draft genome
We generated a (diploid, chordata, highly heterozgous) genome using PacBio and we wanted to see whether it contains lineage-specific duplications (paralogs, basically). The genome is not in Ensembl ...
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How to install DnaSP on a Mac
I need to install DnaSp, a nice GUI originally written for Windows for the population genetics of nucleotide sequence data.
However, its not working on my mac. I'm using wine to install it using these ...
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what percentage of the human genome is MAPQ=0?
When doing Illumina 2x150bp sequencing of genomic DNA, and after aligning the reads to GRCh38, what percentage of the non-N fraction of the human genome is MAPQ=0? This is, what part corresponds to ...
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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 "...
4
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1
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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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How can I use Arlequin via the command line?
I've got a decent knowledge of programming (incl. bash scripting) but I fail to understand how Arlequin works. Could you please help me with a very simple reproducible example on how to use Arlequin ...
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What is the NCBI's definition of an "atypical genome"?
Using the new NCBI Datasets platform, you can browse the collection of genomes associated with one or more taxa. For example, searching Pseudomonas aeruginosa returns 19,878 genomes as of 29 March ...
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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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1
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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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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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1
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How to promote assemblies into genomes in NCBI?
Note: I've never submitted an assembly/genome to NCBI, so excuse if my perspective is flawed.
I'm working with Drosophila subobscura. (spring fruit fly)
I see here https://www.ncbi.nlm.nih.gov/data-...
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Do RepeatModeler results contain functional domains?
The repeat families predicted by RepeatModeler contain known transposable elements (TEs) and unknown ones.
How do we know whether some of these may actually:
within a functional domain of a gene or
...
3
votes
2
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446
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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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How to get the number of complete phage genomes available on ncbi?
I am looking to establish the total number of complete phage genomes available on NCBI.
I am not looking for any specific type, but want to understand the total diversity available.
How can I perform ...
3
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1
answer
192
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Why do BLASTn and prokka not seem to be searching the whole fasta file?
When I use blastn and prokka (I will detail exactly how I did so below) on a 2.8 million bp fasta file I get output start/end numbers that do not seem to cover the entire genome.
Starting with a ....
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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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