Biostar

34,887 results • Page 1 of 698

I am trying to use GRange for mapping snps to gene around 100kb. But I do not know how to download homo sapiens gene locations file including ensembl gene id, chr, start and

SNP biomart gene

updated 6.0 years ago • Huichen03

I am looking at the output of a gene fusion detection tool (genefuse), and part of it: "ALK_ENST00000389048.7:exon:20|-chr2:29223527" has the nomenclature with...chr or -chr, at first I thought that it could be the strand direction but then I saw that in the same file there is the strand direction...and they can be different (-chr can be associated with reverse or forward strand and sam…

genefuse gene fusions chr

updated 2.1 years ago • bio_elle

id=NM_000304.3&db=nuccore&retmode=html][1] On this page I am getting sequence of gene (last part of page ORIGIN) and also table of features. For next step I need to assign whole sequence to chromosome location...this page, which can be accessed from link in feature table in [1]: [https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=full_report&list_uids=5376][2] …

NCBI genome gene python

updated 7.3 years ago • stanedav

Hi. I wonder how to convert chromosome locations to gene symbols. An example of chromosome locations name is 'chr1: 44959708-45072070'. There are many chromosome locations...I want the chromosome location names to gene symbols. Should I use 'biomaRt' package? If I need to use the 'biomaRt' package, how can I change the example...chromosome location name to a gene symbol? Please help me

symbol location chromosome gene

updated 11 months ago • sooni

I have a list of Genes (Ensemble ids). I need to find their locations in the human chromosomes. Information that I need- Start location Stop Location...Length I have tried ShinyGo but got only a graph with the location of genes on the chromosome but not exact locations

Chromosome Mapping Gene Chromosomal-Mapping

updated 4.0 years ago • spriyansh29

Hi all, it is the first time I am doing ChIPseq (I used Galaxy). I obtained a list of enriched genes and their locations. But when I want to see (graphically) the reads, I use the BAM files in IGV. The point is that the location...of the given genes by Galaxy and the location of the genes in IGV is a little bit different. I always used "mm10" as genome reference For example

ChIP-Seq

updated 3.3 years ago • rbravos87

Hi, Is there a way to get information about the location of a human gene in GRanges format (in R) when I have the Gene Symbol and/or Ensembl ID and/or RefSeq Gene ID? Thanks in advance

gene GRanges R human Locus

updated 22 months ago • JW

i have to annotate some data. therefore i need all genes with start and end position located on the mouse chromosome 8 between positions 10.000 and 1.000.0000 (this is just

gene genome R

updated 3.7 years ago • new in gene annotation

Hello! I started a gene enrichment analysis (I haven't done this before), and I have a dataset that contains the gene expression data. This data set...has a column with the gene names. However, there are some entries in that columns, which represent chromosome locations instead of gene names. I want...to find the gene closest to these chromosomes locations. I'm using R 2.15.2 (if that helps). …

gene R

updated 20 months ago • D H

I am trying to get gene locations from a list of genes of interest. As far as I know, it is possible to find them by using ensembl biomart. After selecting...gene start and end for as attributes, I get the values. However, I found that the locations are different from those provided...by NCBI gene (considering for both GRCh37.p13) Do you know the reason? How do you get gene locations from a li…

gene

updated 8.9 years ago • ciclustigu

I want to map the location of some gene families on a few plant genomes/ chromosomes. These genomes are not available in Ensembl. 1. How can I map...the location of my gene of interest on chromosomes/ genomes of plant genomes/ chromosomes using syMAP? 2. what are the other tools

gene genome

updated 8.5 years ago • mirza

I'm trying to create a figure which visualizes the locations of NBS-LRR genes on chromosome 1 on the watermelon genome based on the watermelon sequencing genome paper here...Essentially, I want to create a chromosome map of locations of specified genes for a figure. I've tried to set up the watermelon genome as a database for BLAST, and while it did...give me the numeric location…

RNA-Seq genome alignment blast

updated 8.4 years ago • kevluv93

Hello community, I have a data set (.txt format) that consists of chromosomes and locations like this for example: NC_031974.1- 35234789 NC_031974.1 - 32458 NC_031972.1 - 458920 ... ... ...etc All these unique regions...differentiated between my sample groups. My final goal is to find out what/where are these locations (which genes? are exons/introns/promoters? etc). I am working on the …

gene mapping chromosome coordinates

updated 6.6 years ago • ioannis

Is there a download-able file on UCSC database that gives the information on gene locations (the chromosome ID for the gene, and the base positions) for a given organism ? I want to know the distance (in bp) between...certain genes of interest for Xenopus genome. Is there any other way to achieve this in the genome browser

gene ucsc annotation

updated 10.7 years ago • anuragm

Hi guys, I have a VCF file with SNPs located on the whole genome and I want to identify those that are located on genes. I have converted VCF file to Genotype matrix...and wrote a python script that goes through both GM file and GTF one to find SNPs located in genes. But this takes a huge amount of time. Does somebody know if there exists a standard tool that solves my problem

SNP vcf

updated 7.3 years ago • valerie

Hi Folks, I wanted to know if there is a way to get the cellular location for the genes lists and get their general functions

gene

updated 24 months ago • shah.khyati231

In the genbank format data of gene annotation, usually I can find genes with location like this: [42764:>153205](-) It means that the gene start from 42764 and...end in 153205 or further. Why gene location can not be precisely reported? Also, if I check this gene ("ABR") in UCSC, it will give a lot of gene locations, even in...the same chromosome! (see: http://goo.gl/3er7BR) These…

gene-annotation genbank gene-location

updated 23 months ago • Chen Sun

I have been struggling to find a automatic or programming tool that I can filter and keep the genes that are located or sublocated in nucleus. i have 1000 genes so it is hard to go to uniprot and check one by one. any other

genomics

updated 15 months ago • Bioinfo

Dear all, I am Amrendra, how i can fine location (on chromosome, or locus ) of my gene? and how make it structure means where what promoter will be found and all info

genome Assembly

updated 10.0 years ago • amrendrambiotech

I have an extended list of gene locations (chr#, start and end site) with respect to hg19 as extracted from not very specific alignments. I would like to find...I would like to see what genes fall between each.. indeed, if I had just a handful, I could go to genome.browser and just look there and jot down the genes...as I have > 20,000 of those and not all of them fall perfectly within the…

genomic-location hg19

updated 21 months ago • BioProg

Hi, I want to compare my ChIP-seq read distribution (Human, T47D cell line, hg18) in gene-rich and gene-poor region. What approach would be the best to define this location, or simply, from where I can get these gene...rich (or euchromatin) and gene-poor/gene-desert (heterochromatin) location bed file? thanks, Shumon

sequence genome chip-seq

updated 11.8 years ago • Shumon Shumon

Hi Guys, I have a question regarding the annotation of SNPs. I have list of candidate SNPs with chr ids (file 1) and the their positions and another file (file 2) I have a gft file with chr id, gene positions (start and stop) and genes...names. I am looking to fetch the positions of SNPs (file 1) in between the positions of genes (file 2). I tried bedtools however I could not file the command. P…

Bedtools Genome SNPs

updated 3.0 years ago • Kumar

Dear all, I have a list of sgRNA that were designed for CRISPR experiment and their corresponding gene (symbol). I'm trying to compute a percent peptide score, that is the location of these guides along their target. I need to find...a way to align all these sequences along their target and output the location of the alignment as well as the size of the gene. I though about using a shell scri…

alignment

updated 7.6 years ago • sd74y28r

I am interested in finding the location of housekeeping genes on the human genome, preferably build hg38. Where can I get this? Thanks

gene

updated 3.1 years ago • koen.vdberge

How I can find plant genes location on chromosomes? Kindly guide me I will be very thankful for this kind act

genome gene

updated 7.0 years ago • 15003011

of the same species (Funji) and for each sample, I have three multifasta files containing coding genes (CDS) involved in pathogenicity. Could you offer me a tool that would allow me to locate these genes on the chromosomes...of the reference genome. My goal is to locate the distribution of these genes from each sample on the reference genome. Thank you in advance

localization alignment sequence software genome

updated 5.2 years ago • kamel

I have some genes list and I need to find the chromosome position of those genes. I found 2 web service for this, [ncbi][1] and [ensembl][2]. As you...can see, I search for the gene location TP53 and both website and they give different locations. ncbi location: chr17:7668402-7687550 GRCh38.p7 ensembl...location: Chromosome 17: 7,661,779-7,687,550 GRCh38.p10 Now the locations a…

Assembly

updated 7.0 years ago • akij

Hello, I am trying to find the promoter of a mouse gene Thy1 on the UCSC mm9 genome? I am quite new to bioinformatics so I do not know how exactly to go about finding the location...Hello, I am trying to find the promoter of a mouse gene Thy1 on the UCSC mm9 genome? I am quite new to bioinformatics so I do not know how exactly to go about finding the location of the promoter. I understand that I …

promoter Gene igv

updated 2.2 years ago • karthik

I would like to pick a 1000 random locations in the human genome (say hg19 assembly) and get a list of the genes closest to them. Can you suggest how I can go about

gene

updated 7.2 years ago • sumithrasank75

If I have a two gene sequence and I Wnt to find this gene location on chromosomes of total nine plant genome how it possible Ensemble not contain...is also helpless Please suggest me any platform for doing genome wide analysis for finding exect gene position on chromosomes

R genome gene alignment sequence

updated 5.2 years ago • Mehar Imran Zafar

Hi, I'm trying to extract gene location information for certain genes across multiple bacteria. Currently I'm using this set up to retrieve the gene...the start and end point of a gene on the sequence. It is my understanding that with the use of `SeqIO.parse` each `gene` in the `record` comes with features, including...features for the start and end point of the gene. Below is the output of a ra…

python biopython EUtils

updated 14 months ago • Zoya

Hello all, How to use matlab bioinformatics toolbox to get Molecular Location (start/end) of a gene on chromosome? example: Use a matlab function to get start/end of gene BIN1 on chromosome 2 Molecular...Location on chromosome 2: base pairs 127,048,022 to 127,107,399 Thanks in advance

matlab chromosome gene start end

updated 8.1 years ago • marwa.cs91

I am trying to make a gene location file: Gene_Name Chromosome Start End So that I can run a program that maps SNPs to genes for burden analysis. My...is that UCSC table output gives transcripts, and multiple transcripts can be attributed to a single gene. How do I consolidate things so I can end up with a "one gene one genomic interval" model. bests, JFK

genomics genome sequencing SNP burden

updated 3.4 years ago • jon.klonowski

I have a bed file containing genomic locations and A or B compartment annotations, how do i find the genes in these location from this bed file. I was doing a hic data

fanc Chromatin conformation Hic hic

updated 5 weeks ago • naveedhasan2000

I've got a list of codding genes and I would like to get the cellular location of the expressed proteins, all at once. I already looked up on uniprot but

protein Uniprot RNA-Seq cellular-location

updated 24 months ago • carolinapr.rocha

I am working with a duplicated set of genes. The duplicated genes can be divided into three sub-families, let's say A, B, and C. A and B sub-families are ancestral and have...multiple genes located as tandem array in chr25, C is another sub-family located in chr7. It is clear that C evolved from A or B. Phylogeny...with A, B and C shows Genes of A and B sub-families are basal to C. I want to find…

gene evolution Duplication

updated 4.5 years ago • mjoyraj

the following question already asked in biostar (http://biostars.org/post/show/53561/python-finding-gene-closest-to-a-given-location/). Let us say I have a list of genomic regions (as a bed file), and also a list of genes (as a bed file). For...each genomic region I want to find the 5 (or N to be general) closest genes. How would I try to do that? Any suggestions? Thanks

intersect bedtools

updated 11.6 years ago • dfernan

Hello! I'm trying to identify gene names for the list of SNP (GWAS result) and have some inconsistencies. For some SNPs gene names were identified using BioMart...package in R (by BP - if it is located inside the gene and #chr - the same as gene). For these SNPs I make a plot in LocusZoom and get a list of genes. And not always...gene which was identified with BioMart is included in the list o…

locuszoom biomart

updated 6.8 years ago • alioniya

I have about 3000 genes list and their chromosome locations(start and end). Some of the locations have negative positions as you can see below...in the table. I think this mean these genes are position referenced from negative strand. I need to extract these genes from VCF file, but there aren't any negative...location in VCF file. Can someone please explain me how this issue could be addressed w…

VCF extract vcf chromosome location gene location

updated 8.0 years ago • MAPK

Hi, I would like to get all the chromosomal location information for all genes in humans for both GRCh37 and 38. How can I do this with a Python script? Thank you

gene python

updated 3.7 years ago • magnolia

Hi Friends, i am using grep command for gene location. But grep command automatically remove gene duplication and output file without gene duplication location

R RNA-Seq sequencing

updated 3.6 years ago • abdullahpadana

Dear all, I need to find locations of protein products of a certain list of genes. For example, TLR1(toll like receptor 1) locates on the cell membrane...Is there any database can realize this goal? I know uniprot subcellular location. But it seems only 400+ genes are in the database. Is there any other database or any method I missed please? Thank you

software error

updated 5.7 years ago • Yingzi Zhang

I'm researching for making coverage of SRY gene on male samples. However, from what I read the location of SRY gene on GrCH37 is chrY:2,654,896-2,655,723 (reverse strain). But...from what I search the location of Yp11.2, the band that SRY gene located is chrY:3,000,000-11,600,000. I guess that the location of SRY gene is on the reverse

NIPT

updated 2.5 years ago • khanhlpbao

respectively. I have a reference genome in both fasta format and EMBL format (annotated). How can I locate my indels in the genome based on reference? I want to find where eaxctly my indels are (e.g. in which gene or intergenic

indel annotation

updated 11.7 years ago • bioinfo

How can I search & locate the snp / rs number for H1069Q and G1267R snps on ATP7B gene

gene

updated 11.2 years ago • Inquisitor

Hello, I'm trying to estimate the methylation of the cg sites located on the promoters of some genes. So i have a csv with the cgsites and their beta. I have a list of genes. now I'm trying to find...the promoters of said genes. Taking for example "TSPAN6", going to the ensemble website, I see the promoter tagged as Stable ID ENSR00000911389 Type...mart = regulation) but I can'…

R gene bioconductor biomart

updated 3.8 years ago • Will Yam

I am very new to RNA-Seq. I am trying to align my samples with STAR. I am generating the genome index myself. Because I was hoping to add the spike-in sequence to the GTF and FASTA files. I am downloading the GTF file from here: ftp://ftp.ensembl.org/pub/release-86/gtf/mus_musculus/ There are 2 GTF files one with CHR in the name and one without. I was wondering which one should I use and how t…

RNA-Seq STAR ensembl

updated 7.1 years ago • rf

HI , I got all human gene region file from UCSC http://genome.ucsc.edu/cgi-bin/hgTables. I find that the same gene is located at different chromosomes...102513726, 102513794, 0 **MIR6859-1** unk unk -1, the MIR6859-1 gene is at both chr1 and chr15, why ????what happened

gene rna-seq next-gen genome

updated 5.8 years ago • winter_li

So I know Consensus CDS (CCDS) has the genomic locations of exons, however, only of the exons in the CDS. Everything before or after is not included. NIH variation viewer has...those (kinda-) radio buttons next to the gene name, and when you hover over them, you do get to see the genomic locations of the exons. But this method isn't very scalable...Does anyone know an easy, scalable way of ret…

exons genomic-locations genome

updated 2.3 years ago • biodatascientist

Hello everyone I want to add a picture to my article and summarize published mutations of a gene and its protein. I tried ucsc or NCBI but i couldn't find exact location of that mutations there because It was complicated...for me . for example I got no results after i searched c.599C>A in https://www.ncbi.nlm.nih.gov/gene in Genomic regions, transcripts, and products Tab. I need a datab…

gene

updated 5.9 years ago • yoosefyud

34,887 results • Page 1 of 698

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