Questions tagged [gene]
Use this tag to refer to the gene sequence/coding part of the sequence.
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How to analyze gff file?
I have a genome annotation file for in gff file format for a certain lizard species, how would I go about analyzing a specific gene (sulf1) to see if it is functional, I wanted to specifically look at ...
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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, ...
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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 ...
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Extract data from genome
Is it possible to "extract" genes and, after that proteins and other natural compounds from a not-so-well-studied plant whose genome data is available on NCBI?
What other useful information ...
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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 ...
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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 ...
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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:
...
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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 ...
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47
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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.
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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:
...
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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 ...
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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 ...
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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 ...
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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%...
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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, ...
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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, ...
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345
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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:
...
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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):
...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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47
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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 <...
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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 ...
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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 ...
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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 ...
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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 "...
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Converting Gene Symbol to Entrez ID in R
I analyzed a GEO dataset and found 99 DEG.Now I want to analyze functional enrichment analysis and for that reason I have to convert my gene symbol to entrez id.But I cannot do that,I tried but my ...
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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 ...
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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.
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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 ...
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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 ...
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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'...
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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 ...
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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 ...
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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 ...
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Converting gene symbols between species
I have a list of genes in a mouse model
How I can find the equivalent gene symbol/name for human from them?
This is my list
...
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Positive marker and negative marker in scRNA-seq datasets
I am learning about the marker genes and clustering by Seurat in scRNA-seq datasets. However, I am confused about the term positive marker and negative marker. What I understand is the marker genes of ...
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where to find sample contig data
Where or How can I find contigs? I am trying to learn Bioinformatics and I want to make a reference-based gene search. I also want to align contigs with a given reference sequence. From NCBI other ...
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Important genes beyond PAM50 for breast cancer classification
Note: this question has also been asked on Biostars
I am currently trying to complete a Breast Cancer Classification task using Neural Networks. I have experimented with using my full dataset of gene ...
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How can I associate centrality score of genes(vertices) in a GRN with the probabilistic model in terms of cause and effect?
I'm learning to build Bayesian Network Based Modeling of Gene Regulatory Network of Cancerous Cellular Cells. So far, I have learned to form a Bayesian Network based on nature of genes(i.e Functional ...
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Differential gene expression analysis of time series with replicates
I have a dataset that has two groups, perturbed vs control. Each group has 3 replicates. Each replicate has 8 time points. How do we do Differential gene expression analysis to find significantly ...
