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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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How can I filter variants in a VCF file based on size?

I have a filtered VCF file with indels (no SNPs). Does anyone know of a easy way to use bcftools/vcftools to filter out small or large indels (I'm interested in indels between 50-100bp in size)? ...
bioinformaticsuser9074's user avatar
1 vote
1 answer
23 views

Why is mtDNA not labelled as such for many organisms?

Also posted on biostars While I was searching the genomes of some eukariotic organisms (fungi,plants,protists) even though I knew that they had mitochondrial DNA,when I searched their genome structure ...
George X.'s user avatar
3 votes
1 answer
64 views

How to prove correlation between gene expression and functions using omics data in bioinformatics?

I am new to bioinformatics, coming from a background in mathematical biology. I am currently participating in a project where the Principal Investigator (PI), who is a biologist, has tasked me with ...
LOVEMATH's user avatar
-1 votes
1 answer
26 views

Concatenate multiple fasta files into individual files per unique entry

I have several splitted fasta files like this: TK273759.fastaaa TK273759.fastaab TK273759.fastaac TK273759.fastaad TK273759.fastaae I want to concatenate these ...
Sufia Akter Neha's user avatar
-1 votes
1 answer
34 views

Where can you download functional domain labels of the human genome?

I'm visualizing where mutations occur in a gene, and would like to add functional domains to the plots. I have some trouble locating sources to download data on functional domains. The dataset should ...
Sofie's user avatar
  • 1
3 votes
1 answer
79 views

How to annotate a bacterial genome automatically?

We recently got some shotgun sequencing results from a soil bacterium. And we have obtained some contigs which have some genes of interest. Is there a way to automatically annotate the whole sequence (...
Irfan's user avatar
  • 81
1 vote
0 answers
120 views

bwa mem hangs after a few thousand reads

I am trying to align a bunch of paired sample fastq files using bwa mem. My original command was: ...
padakpatek's user avatar
1 vote
1 answer
30 views

Annotation result for phylogenetic analysis shows no common evolutionary gene in contigs, can i change the contigs?

I'm currently doing my thesis with the topic of phylogenetic analysis and is taking references from the previous person in my university (who have done the same topics but different species). They ...
Ayu Rani's user avatar
1 vote
0 answers
42 views

How to use HGTECTOR tool for identifying HGT genes in a bacterial genome?

I wanted to know the HGT genes in a Metabacillus strain and I noticed that several papers use HGTector for this purpose. I installed HGTector through conda and tried to download the database for ...
K_081's user avatar
  • 149
2 votes
1 answer
74 views

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.
Mudith Ekanayake's user avatar
0 votes
0 answers
44 views

How do you download metadata for TCGA pathology slides

I downloaded the TCGA pathology slides for the SKCM project and the files are all a name such as "TCGA-3N-A9WB-01Z-00-DX1.A9950ED4-9480-455C-AE0D-8E076D4DA432.svs". How do you get the ...
DeepLearner123's user avatar
4 votes
1 answer
45 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
1 vote
1 answer
50 views

Identifying the promoter on the reverse strand using visualization software (seqmonk)

I feel like this might be a really silly question and I've been going back and forth for awhile and I think confusing myself- so sorry if this is dumb. I am using Seqmonk to visualize genes in an ...
user18170's user avatar
3 votes
2 answers
220 views

How to analyze GC content of fasta file?

I have the assembly file of a certain lizard species, I wanted to recreate Fig. 2 of the following paper, which compares the GC content distribution over 5kb windows, how would I go about doing this? ...
JohnDoe23's user avatar
1 vote
1 answer
66 views

What options are there for visualising DNA sequences?

I typically see several ways of visualising DNA sequences and I would like to know when (best) to use them? For example, I sometimes see the letter codes GATC, sometimes I see colours, sometimes I see ...
Scott McKenzie's user avatar
3 votes
1 answer
133 views

Why doesn't bedtools getfasta pick up the first base?

I am using bedtools getfasta to convert genomic coordinates to sequences. I feed it a bedfile containing say chr1 s.start s.end. When I check the sequence output, it does not include the s.start base. ...
venkatesh war's user avatar
0 votes
0 answers
30 views

Error while opening xmfa generated by progressiveMauve

I used commandline progressiveMauve to align two genome .gbk files. The alignment was successful. But when I try to visualize the final .xmfa file with Mauve, I get the following error. ...
venkatesh war's user avatar
1 vote
2 answers
65 views

Why does my HWE QQ plot have extreme deviation and what does it mean?

This question was also asked on Reddit I have recently completed my thesis and one of the comments was that I report on why this graph looks this way. I have tried to find a reason but the closest I ...
Shelby Labuschagne's user avatar
0 votes
0 answers
23 views

Gene Expression Database for Psychological Disorders

Is there a comprehensive database available online of gene expression across the brain taken from individuals with psychological conditions? Resources like the Allen Institute's Human Brain Map (link ...
Lambda's user avatar
  • 101
1 vote
1 answer
289 views

How do I add reference/alternate alleles to my vcf file?

Here are the first few columns of my VCF v4.2 file. As you can see, the alt allele is missing. The VCF's refs and alts don't correspond to the reference genome. #CHROM POS ID REF ALT 9 77051 ...
BigMistake's user avatar
1 vote
1 answer
144 views

How do I calculate inbreeding on a single VCF file?

I would like to know the level of inbreeding for a single sample VCF file. I'm agnostic to the specific method of measuring inbreeding; any should work. However, I'd like to avoid having to specify a &...
BigMistake's user avatar
0 votes
2 answers
77 views

Human genome similarities

As far as I know, we as humans share 99.9 similarity in our genomes. Further, we inherit 50% of the genome from our parents. So, it is correct to say that parent children have a 99.95% similarity in ...
TPArrow's user avatar
  • 117
2 votes
0 answers
51 views

Running Genome Scale Metabolic Model but with different concentration of medium composition

I want to run a simulation with COBRApy for my bacterial Genome Scale Metabolic Model (GEM). I want it to run on different concentration of medium composition such as 0% NaCl, 10% NaCl, and 20% NaCl. ...
raysteven's user avatar
3 votes
1 answer
131 views

Extract compounds/proteins from plant genomic data

I want a process by which I can identify genes within plant genomes; i.e. a process that works for all plants, not just for a single species. I'm wondering, if, by bioinformatic means only, it is ...
Sorin Trimbitas's user avatar
1 vote
2 answers
72 views

Extract data from genome

This question was also asked on Biostars 3 months ago, i.e. a long time - so its perfectly reasonable for the question to be asked here I started studying bioinformatics and I enjoy it a lot (I'm a ...
Sorin Trimbitas's user avatar
1 vote
1 answer
29 views

How important are the homozygous variants that get unnecessarily deleted using liftover?

I'm referring to the text described here: These tools [NCBI remap, CrossMap] operate only on the sites present in an input VCF, and return the representation of those sites in a new genome assembly. ...
BigMistake's user avatar
0 votes
1 answer
62 views

Is a human genome file with reference as NCBI37 the same as hg19?

This question was also asked on Biostars In other words, are NCBI37 and hg19 synonymous? I can't find much information for what NCBI37 is in a human (not mouse) genome. The VCF is from a lab ...
BigMistake's user avatar
1 vote
0 answers
52 views

What is the current state-of-the-art for classifying the ancestry groups of VCF files?

I'm wondering which tool or program is: Most updated; doesn't use a superseded algorithm Runs very quickly (ideally, under 30s per VCF file) Able to be automated in some way for a large number of ...
BigMistake's user avatar
3 votes
2 answers
284 views

Where do I get a large reference VCF?

I would like to download a large .vcf file containing many (hundreds or thousands) of samples. Ideally, I would download different population-specific .vcf files, but the ability to sort/filter by ...
BigMistake's user avatar
4 votes
1 answer
99 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
2 votes
2 answers
205 views

Improving prokaryotic assembly with other contig/scaffold-level data?

I have what at first sight appears to be a high-quality MAG (~10 pieces, high completion%) that I built from a hybrid assembly (Illumina + Nanopore data) from a cyanobacterium. Workflow: Quality ...
Laura's user avatar
  • 909
2 votes
1 answer
62 views

Availability of information on genes in Gnomad VCF data

I was wondering does the gnomad genome data that is downloaded in the vcf format on variants contain information on what is the nearest gene and is the genomic location available exome/intron? if yes ...
agnesa rivkin's user avatar
0 votes
1 answer
85 views

Allele frequency gnomad data

I noticed that some gnomad SNPs have allele frequency =0 and some are just not found : No genes were found in this region. what is the difference between them : for example:Y-10010520-10010520. Is all ...
Eliza Romanski's user avatar
1 vote
4 answers
144 views

Grep peculiar pattern inside a file

I would like to grep everything inside the second square bracket of a file: ...
Marco's user avatar
  • 161
1 vote
1 answer
56 views

Why do Illumina 850k/EPIC arrays ignore CpGs which are "GC" in the forward strand?

CpGs are symmetrical, in that a CG sequence on the forward strand is hybridized to a GC --- and both dinucleotides on each opposing strand are CpGs dinucleotides which can be methylated. Conversely, ...
ning's user avatar
  • 141
1 vote
1 answer
55 views

How to identify mutations in a viral genome

I have a fasta file with multiple sequences comprising 38 sequences. The length of the sequences are around 11000 bp. How can i get changes in the genomes based in a reference genome? (aa subtitutions ...
Gerald Vasquez Aleman's user avatar
1 vote
1 answer
90 views

Allele effects by parental-origin estimated from genotyping array data

We are dealing with relatively large family data (> 1,000 trios) with genotyping array data. We would like to see the allele effects on children separately of mothers, fathers, and children, as in ...
PenguinPartyH0's user avatar
4 votes
1 answer
64 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
  • 249
3 votes
2 answers
286 views

Searching for HLA-B in DNA results

I'm trying to find the HLA-B*15:01 variant in my DNA results, prompted from this research paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8142661/#:~:text=HLA%2DB*15%3A01%20is%20strongly%...
stan's user avatar
  • 131
2 votes
1 answer
77 views

What is the best way to process yeast genomes?

I have obtained several hundred raw, unassembled yeast genomes from NCBI and I am looking for advice on how to process the genomes for downstream analysis. I have a reference genome (S288C) to use for ...
rimo's user avatar
  • 963
1 vote
1 answer
94 views

Lower case vs. upper case nucleotids in sequence vs. dots at the end

What is the difference between lower case and upper case nucleotides in a sequence? My other question is what are the dots at the end of the sequence? Some examples are shown below: GGgG,GGgG,GGgG,...
David Khutsishvili's user avatar
2 votes
2 answers
171 views

Bacterial genomes and snpeff warnings 'WARNING_TRANSCRIPT_NO_START_CODON'

I annotated a bunch of genomes with snpeff. And although the original reads' qualities and the matches with the reference genomes were quite high, I see the above mentioned warning in almost every ...
Anti's user avatar
  • 153
2 votes
0 answers
53 views

Is there a way antiSMASH can be used to screen a large number of genomes just for one type of biosynthetic gene cluster?

When we use antismash command with the genome sequence file as follows: antismash GCA_002095535.1_ASM209553v1_genomic.gbff it screens the genome for all the ...
snap_v's user avatar
  • 21
2 votes
1 answer
76 views

Is there a way to extract spike sequence from a Sars-CoV-2 complete genome (preferably in Python)?

I have a complete genome sequence of a Sars-CoV-2 variant, but I am only interested in the Spike sequence? I should note that I am not a biologist (nor bioinformatics). The complete genome looks like ...
mac179's user avatar
  • 121
1 vote
0 answers
42 views

System specifications for NGS data analysis

I have a 3.7 GB whole genome data of a eukaryote, for which genome assembly, gene prediction, and annotation steps have to be performed. In some time I would also need to analyze the transcriptome ...
Shakunthala's user avatar
3 votes
1 answer
90 views

How to make pan-core genome curve through command line on linux?

I´m working with a dataset of 566 genomes to analyze a pangenome. So I was working with PANWEB to create this pan core genome curve, however, there is too much sequence to work with this webserver. ...
Someone_1313's user avatar
2 votes
0 answers
11 views

Flux balance Analysis, Result interpretation, solver Solver Heuristics

i am new to modelling of cellular networks, and I have two basic questions, regarding the result interpration. I am using the COBRAToolbox to do a flux balance analysis of a whole genome scale model ...
Martin Welte's user avatar
0 votes
1 answer
51 views

Target genes for piRNA

Where I can find a database or tool to give me the target genes of PIWI (piRNAs) in human? I found one but works for worm like <...
Zizogolu's user avatar
  • 2,148
0 votes
0 answers
85 views

Help me to calculate Heaps Alpha value from the roary pangenome pipeline result?

I need to know whether my pan-genome is open or closed. For that, I need to calculate the ...
Kumar's user avatar
  • 109
1 vote
0 answers
25 views

Why does gene count increase drastically after scaffolding with Hi-C data?

I have a conceptual question. I have a diploid, outcrossing plant genome assembly of ~1.1 Gb size. The original assembly is generated from PacBio reads. After genome annotation with the ...
Anik Dutta's user avatar