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Questions tagged [gene]

Use this tag to refer to the gene sequence/coding part of the sequence.

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What is difference between gene and CDS in the gff file?

I'm investigating bacterial genome. In GFF file, it includes gene, CDS, tRNA or something like that in region fields. What is the difference between gene and CDS? Thant you in advance.
uri's user avatar
  • 43
-1 votes
0 answers
29 views

How do I get the gene annotations as a text file from a genbank file?

Also posted on biostars I have a genbank file and I need the following details about the gene annotations in a text file ...
Minho's user avatar
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1 vote
1 answer
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Best reference book for basic concepts when working with bioinformatics

I'm starting to study Bioinformatics, I already have basic knowledge of Biochemistry and Genetics, but I want to buy a reference book, to use when I forget a concept (I'm a Computer Science student, ...
CaioBonani's user avatar
3 votes
1 answer
66 views

What is it about gene names starting with "LOC"?

I was struggling to use AnnotationDbi to change my ensemble ID to gene name, for datasets of three different species (human, canine, mouse). Among gene names for all three species there are genes with ...
ToTheMoon's user avatar
0 votes
1 answer
39 views

Gene ensemble vs Hugo id

Hi I have been recently struggling with the gene annotations and changing gene ID to ensemble ID. While I was doing that there were some genes for the same species that had the same gene ID but ...
ToTheMoon's user avatar
0 votes
1 answer
71 views

conducting a ttest on a board of 1000 genes in 50 peope divided into to groups(A and B). pvalues are different each time

I am struggling in conducting at test on a board of 1000 genes in 50 individuals divided into to groups (A and B). I have a dataset of 1000 genes of two groups of people (total individuals=50) group A ...
biostefania's user avatar
0 votes
0 answers
69 views

Convert genotyping results to vcf or other plink formats

I used a Genotyping software called T1K to generate KIR genotyping, the output file contains genes and alleles for each sample, how can i convert the results to a vcf file or other formats which can ...
Alice Yan's user avatar
0 votes
0 answers
30 views

Need to make circos plot from Enrichment data

I have a list of genes and their associated pathways. The data was generated using Partek. The data looks like this - Gene_in_list Gene_set Description Enrichment score P.value Gene1 hsa Disease C ...
Karthik Nair's user avatar
2 votes
1 answer
57 views

How to rearrange gene ontology obo file?

I have a gene ontology obo file, and would like to rearrange the obo format file in a single column to a text file in three columns comprised of 'parent (id:GO:xxxxxxx)', 'child (is_a: GO:xxxxxxx, ...
ojikj2023's user avatar
1 vote
1 answer
53 views

Gene Set Comparison Without Expression Data

I have been looking all over the web to find some answers to my problem but unfortunately, I was unsuccessful. I wish to determine whether an a priori defined set of genes in my case genes associated ...
Eliza R's user avatar
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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
0 votes
0 answers
22 views

How to find the correlation between two genes and their separate overall survival outcome?

i am struggling to find the correlation between two isoforms and their survival outcome. i do have a dataset that is a cohort for thousands of genes and am only interesting in two which they should be ...
hind.sami's user avatar
2 votes
2 answers
113 views

How to get the nucleotide sequence for protein NCBI accession code, programatically?

It is a lot easier in my work to do blast searches against protein databases when I can, since I work with distantly related organisms. But sometimes, I need to work with the actual nucleotide ...
Laura's user avatar
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1 vote
0 answers
104 views

How can I calculate the coverage of a gene in exome sequencing / calculate coverage per gene?

I have a bam file of whole exome human data. I now want to check coverage of a list of genes in my data. Basically, I want to get output like, for example: ...
Ani's user avatar
  • 11
2 votes
0 answers
53 views

Custom-made kraken2 catalogue

I am looking for instructions on creating a custom-made kraken2 catalogue from the sequences of my choice and the corresponding phylogenetic tree in newick notation. I will appreciate an input on ...
Roger V.'s user avatar
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0 answers
60 views

SKAT method in R

I have data that looks like this: 3 column SNPs their gene based on Annovar and a p-value for every SNP. What I would like is to aggregate the p values for every gene. ...
liza's user avatar
  • 29
0 votes
1 answer
96 views

Is my reference sequence too small?

I'm trying to map ONT long reads to a portion of a gene I'm looking at. The region is about 25bp long. When I search for the region in the document it pulls up the sequence in every read but when I ...
rimo's user avatar
  • 963
1 vote
1 answer
207 views

Converting a Dante Lab VCF file

Is there an easy way to grab the rsids (hg38) of a VCF file? I know one of the tabs can contain RSIDs, but this file doesn't contain any. I have a software I created for mapping 23AndMe DTC testing to ...
Shay Maor's user avatar
2 votes
1 answer
437 views

Getting nearest gene from SNP data using SNP ID, CHR, and BP

I have data from a GWAS that provides me with the SNP, Chromosome, and base-pair. My data set has thousands of SNPs. What is the easiest way to find the nearest gene for each SNP using this ...
cjsterne's user avatar
1 vote
1 answer
129 views

How to get a file with the introns of a gene?

I was able to get the exons of a particular gene as a fasta file from the NCBI genome viewer. As for introns I only found a bed file that showed where the intron starts and ends, along with its ...
venkatesh war's user avatar
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
68 views

Mismatch between mutant gene and reference gene outside the site of mutation

I am tasked with designing primers for a particular mutant (Target Gene Locus: At1g28490 i.e. SYP61) of Arabidopsis, obtained from Gabi-Kat: The NCBI reference sequence for the genome goes: ...
AvadaMouse's user avatar
0 votes
1 answer
48 views

SNPs location out side the gene

I downloaded exome data from gnomad to get the allele frequency of some SNPs that I'm analyzing. The SNPs are from external resource. Some SNPs (in my data) are not present in the exome data (in ...
Eliza Romanski's user avatar
1 vote
0 answers
15 views

What visualization was used for ICA in the tissue experiment?

I want to run the experiments in mentioned in enter the matrix. For the the plot in figure 3B it mentioned that The relative absolute value of the magnitude of each element in the pattern matrix ...
A.Dumas's user avatar
  • 497
0 votes
1 answer
132 views

Why are genetic algorithm chromosomes represented using 8 bit binary?

I am learning about genetic algorithms. Why chromosomes are represented using 8 bit binary. This arose when I apply crossover techniques to the bits. Please help me to find the answer.Thanks in ...
Julie's user avatar
  • 1
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
1 vote
0 answers
39 views

Comparing common genes and transcripts between Gencode and Refseq

This is a very naive question - I am trying to compare and get the common lncRNA genes and transcripts between Gencode and Refseq from their gff files. Since their gene_id, gene_names are different, ...
beepboopbeep's user avatar
0 votes
1 answer
47 views

Building a group representation of genes' ontologies

I have a list of genes (about 2000) from lines of drosophila subobscura, in the following format: LOC117900589 LOC11788959 LOC11790331 I'm trying to represent this set of genes in a useful way. So, ...
gl00ten's user avatar
  • 249
1 vote
1 answer
499 views

Error of duplicated rownames although there are no duplicates

I have a data frame that I want to switch its row names from EnsembleID (GENEID) to gene symbol (SYMBOL). When I try to switch, I get this error: ...
Programming Noob's user avatar
1 vote
0 answers
136 views

snpEff annotation and variant in a gene

I'm using snpEff to annotate genetic variants. However, the annotation often returns more than one annotation (see below for an example): ...
Anti's user avatar
  • 153
1 vote
0 answers
19 views

Which components must be included in the HDR plasmid?

I am trying to design a plasmid for our knock in experiment and wanted to clarify some technical issues. I wanted to know exactly which components must be included in the plasmid. I know that I have ...
Research HMBR's user avatar
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
42 views

How good does the assembly of an NCBI prokaryotic genome have to be in order to argue gene loss?

NCBI has several labels for assembly completeness - Complete, Scaffold, Chromosome and Contig. Complete would be a circularized genome (or linear, rarely) For a Complete genome it's fairly ...
Laura's user avatar
  • 909
1 vote
2 answers
391 views

Converting .bw files to .fq (fastq)

I am able to convert .bw files to .fq(fastq) manually in Shell, but I would like to automate the process coz I have hundreds of .bw file that I need to convert. Till now, I could think of following ...
Sam's user avatar
  • 19
1 vote
1 answer
407 views

VCF or BAM file for raw data of gene test?

My friend has a VUS (Polymicrogyria with or without VEDS) mutation that was found in her whole-exome sequencing with respect to the phenotype given that time. At present, her doctors have more ...
Suswagatam Rong'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
4 votes
0 answers
46 views

How to summarize multiple exon copy numbers into copy number of the corresponding gene

I have a matrix, sample by exon, containing a copy number value for each pair (sample, exon). I would like to generate a second matrix, sample by gene, where the copy number of the exons is ...
gc5's user avatar
  • 1,783
2 votes
2 answers
47 views

Is there a publication database or search engine offering geneID or UniProtID correlation?

Do we have a publication database or search engine that offers geneID or UniProtID correlation? For example, I search "IPS cells" -> I want to know what genes or proteins are under active ...
Johnny Tam's user avatar
1 vote
0 answers
23 views

How to get a list of all human morphogens?

Gene Ontology provides many genes annotated as taking part in various morphogenesis processes but I want to get a list of all morphogen coding genes specifically. Uniprot does not have "...
Sashko Lykhenko's user avatar
1 vote
2 answers
498 views

How to retrieve fasta sequence after local blast?

I have created a Blast database using a reference genome. Then, I have performed a local blast search in command line using a gene of interest. I have obtained some hits with the usual Blasting ...
Anik Dutta's user avatar
1 vote
0 answers
33 views

How to train annotations tools

I would like to train Augustus, SNAP and GlimmerHMM. I found protein sequences in GenBank and orthodb.org. Furthermore, I found HMM files on busco-data.ezlab.org. ...
user3523406's user avatar
-1 votes
1 answer
29 views

What is meant by transcriptional changes executed by the cell over a time period?

I read the following line in the research paper - The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells: During differentiation, for example, each ...
Deepak Tatyaji Ahire's user avatar
0 votes
0 answers
272 views

functions in seurat to calculate the gene count per cluster

I'm running FindAllMarkers ...
mmpp's user avatar
  • 371
0 votes
1 answer
309 views

Hisat2 compatibility for long reads (Pacbio)

I am working with a high performance cluster computer containing 112 threads. I am trying to align PacBio transcriptome reads against the genome to count the gene number. For pair end read i used the ...
Kishor Kumar Sarker's user avatar
0 votes
1 answer
224 views

Find corresponding symbol for gene used in Seurat

I have a Seurat object ...
Mahta Mira's user avatar
2 votes
0 answers
60 views

Which GWGAS Tool is 'better', MAGMA or LDSC?

I am currently doing a project regarding gene-based analysis and gene-set analysis given a certain GWAS dataset, I only know 2 well known gene-based analysis tool which is LDSC and MAGMA. As of now, I'...
Andreas Adinatha's user avatar
1 vote
1 answer
78 views

The biological meaning of the random variables and the responses in Seurat analysis

In the Seurat analysis, if we suppose that Xg and Xr denote the random variables that associate to the expression level of the gene g and of the gene r, respectively. Let Y and Yv represent the ...
MK Huda's user avatar
  • 163
2 votes
1 answer
52 views

Connection between Detected Genes and The Read Counts

I have been trying to understand the Seurat for analysing scRNA-seq data. It comes to my mind that the main data is organised in the Seurat object with rows as genes and columns as the cells, and the ...
MK Huda's user avatar
  • 163
-2 votes
1 answer
335 views

Getting conventional gene symbol for Seurat [duplicate]

I have a Seurat object made by human single cells I am mapping some genes on that but no sign of expression When I GOOGLE for those genes I see the genes have different names How I know Seurat uses ...
Zizogolu's user avatar
  • 2,148