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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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33 votes
3 answers
26k views

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 ...
Scott Gigante's user avatar
27 votes
4 answers
7k views

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 ...
719016's user avatar
  • 2,324
23 votes
4 answers
15k views

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: ...
story's user avatar
  • 1,573
21 votes
8 answers
5k 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 ...
CCCCoder2's user avatar
  • 319
12 votes
5 answers
357 views

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 ...
Scott Gigante's user avatar
10 votes
3 answers
642 views

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-...
conchoecia's user avatar
  • 3,181
9 votes
2 answers
7k views

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 ...
gc5's user avatar
  • 1,813
9 votes
2 answers
11k views

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 ...
SmallChess's user avatar
  • 2,709
9 votes
1 answer
563 views

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 ...
agapow's user avatar
  • 788
8 votes
5 answers
1k views

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 ...
ShanZhengYang's user avatar
8 votes
3 answers
863 views

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 ...
pwray's user avatar
  • 191
8 votes
2 answers
2k 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. ...
aechchiki's user avatar
  • 2,676
8 votes
2 answers
436 views

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/...
D M's user avatar
  • 181
7 votes
6 answers
2k views

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.
719016's user avatar
  • 2,324
7 votes
2 answers
2k views

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 ...
SmallChess's user avatar
  • 2,709
7 votes
1 answer
2k views

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: ...
Anna1364's user avatar
  • 516
7 votes
2 answers
803 views

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. ...
Titouan Bougouin-Laessle's user avatar
7 votes
1 answer
169 views

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: ...
Anthony Guterres's user avatar
7 votes
1 answer
380 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 ...
Daniel Standage's user avatar
6 votes
2 answers
1k views

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?
AlwaysTrying44's user avatar
6 votes
3 answers
810 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: ...
Zizogolu's user avatar
  • 2,160
6 votes
1 answer
114 views

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 ...
Biomagician's user avatar
  • 2,459
6 votes
1 answer
105 views

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 ...
Jens's user avatar
  • 69
6 votes
2 answers
471 views

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 (...
AudileF's user avatar
  • 955
6 votes
2 answers
1k 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 ...
simusid's user avatar
  • 161
6 votes
2 answers
193 views

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. ...
gagro's user avatar
  • 63
5 votes
1 answer
89 views

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 ...
Pavel Pelan's user avatar
5 votes
6 answers
2k 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 ...
Randoms's user avatar
  • 183
5 votes
3 answers
2k views

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 ...
Eric Brenner's user avatar
5 votes
2 answers
855 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 (...
aechchiki's user avatar
  • 2,676
5 votes
1 answer
8k 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 ...
annabelperry's user avatar
5 votes
1 answer
4k views

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: <...
Biomagician's user avatar
  • 2,459
5 votes
2 answers
876 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 ...
terdon's user avatar
  • 10.2k
5 votes
1 answer
909 views

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 ...
SmallChess's user avatar
  • 2,709
5 votes
1 answer
173 views

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 ...
aechchiki's user avatar
  • 2,676
5 votes
1 answer
2k views

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 ...
Mollie Passacantando's user avatar
4 votes
2 answers
17k views

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 ...
ThisaruG's user avatar
  • 239
4 votes
4 answers
622 views

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 ...
719016's user avatar
  • 2,324
4 votes
1 answer
410 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 "...
Элл Нейгебауэр's user avatar
4 votes
1 answer
94 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 ...
L R Joshi's user avatar
  • 719
4 votes
2 answers
2k views

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 ...
Remi.b's user avatar
  • 203
4 votes
1 answer
104 views

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 ...
acvill's user avatar
  • 613
4 votes
1 answer
49 views

How to get cytoband and gene level copy number from genome wide SNP array copy number data?

I have (human) Illumina genome wide SNP array copy number data. For each SNP genomewide, I have Log R Ratio (LRR) and B Allele Frequency (BAF). What tool(s) can I use to get the integer copy numbers (...
Sylvia Rodriguez's user avatar
4 votes
3 answers
79 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 ...
brian's user avatar
  • 41
4 votes
1 answer
63 views

Replicating VCF Filtering & Trait-Based SNP Extraction Workflow

I'm new to handling SNP genotyping data in VCF format. My goal is to identify significant SNPs linked to a specific trait (like "height") for specific samples in a multi-sample VCF file. My ...
web's user avatar
  • 71
4 votes
1 answer
65 views

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-...
gl00ten's user avatar
  • 269
4 votes
1 answer
183 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 ...
MrTomRod's user avatar
  • 191
4 votes
1 answer
137 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 ...
SmallChess's user avatar
  • 2,709
4 votes
1 answer
159 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 ...
KingBoomie's user avatar
4 votes
0 answers
36 views

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 ...
Life_Searching_Steps's user avatar

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