Biostar

34,947 results • Page 2 of 699

Hi all, I have found some simple sequence repeat (SSR) using BatchPrimer3 tools on some gene sequence of Rice. Now I want to find the location of these SSRs, where the repeat located on the coding or non-coding (UTR) region...of gene sequences, I can do it using Rice genome browser for one gene at the time, but it's time-consuming for many genes. Could you...please let me know how I can perform …

blast genome

updated 10 months ago • coolmsandhu

I have a `VCF` file with `SNPs` and genes subset of `GFF` file (only genes are present). How to extract `SNPs` in `VCF` format located in genes from my data

gene snp

updated 5.7 years ago • Denis

Hello, Given a list of gene names, I need to create a table containing the Ensemble ID, chromosome, start, end of that gene. Example: ## ens_id gene view chr...start end ## 1: ENSG00000243485 MIR1302-2HG Gene Expression chr1 29553 30267 ## 2: ENSG00000237613 FAM138A Gene Expression chr1 36080 36081 ## 3: ENSG00000186092 OR4F5 Gene…

updated 2.7 years ago • cthangav

I have a list of human genes (order matters, since they have been clustered together) and I'd like to see their position in the genome. I was thinking...first axis represent the genome displayed as one chromosome after the other; second axis represent gene list with arrows pointing from each gene to the correspondent location in the genome. Ideally, I hope to see groups of arrows...poi…

genome R

updated 8.8 years ago • Chip

I have some SNPs that I need to find refgene location (non-synonymous, ncRNA_exonic,splicing, etc) given the chr: position:REF:ALT. I have tried VEP tool, but that does not give

SNPs refGene

updated 21 months ago • MAPK

Hello, Can anyone recommend a good tool for translating a list of chromosomal locations to gene names For example: chr1 2000 -> chr2 2008880 -> Thanks! Roni

gene genome

updated 4.1 years ago • haasroni

Can anyone help me with converting amino acid location to nucleotide location? I have the amino acid position with the gene name, and I'm trying to find the corresponding...nucleotide location for the amino acid position. Is there any bioinformatics tools to convert the amino acid location to nucleotide...location? Any help is greatly appreciated, many thanks in advance

next-gen

updated 5.9 years ago • bspriya

genome="Wall_10_chr.fasta" # Iterate through unique chromosomes in the BED file for chr in $(cut -f1 "$input_bed" | sort -u); do # Create a temporary BED file for the current chromosome temp_bed="${chr}_temp.bed" # Extract regions...for the current chromosome and save them to the temporary BED file awk -v chromosome="$chr" '$1 == chromosome' "…

genome awk edditing bash python

updated 3 months ago • Ap1438

Hi,I am new to this research.I am trying to understand how to fetch intron location.I have get gene location and exon location from NCBI, but I am still confused about exon location. My question could be shown as follows...UTR-> intron->exon->intron->exon->intron->3'UTR** Q1: when I only consider intron location, whether I do not consider 5' or 3' UTR as…

gene genome

updated 2.1 years ago • jesselee516

I am getting the chromosome location of a human gene list using getbm. However, getbm can not return some genes' locations, such as "LILRA3". getBM(attributes...4 CHR_HSCHR19_4_CTG3_1 LILRA3 54294391 54301485 But searching the gene manually on NCBI, you know LILRA3 is on chromosome 19. Is this because the ensemble data is not updated or some other reason...solve thi…

gene genome R biomart

updated 4.4 years ago • Feng Zhang

Hello, I'm looking for How to get all locations in the genome of the 5'end of genes (hg19) ? Best

genome hg19

updated 9.1 years ago • Zakaria Benmounah

that I am not a bioinformatics person. I just need to count total number of positive and negative genes located on chromosome in .genes or .gff3 file. Can you please comment how can I do that? Thanks in advance

gff3 htseq

updated 5.5 years ago • arsilan324

What is the preferred way to, given locations in a genome, find the first genes that are upstream or downstream of these locations? I have been looking into processing

python annotation gff parsing ensembl

updated 10.4 years ago • bbio

I have a large set of genes, and need to acquire chromosomal location (in 1p12.2 format) Does anyone know if there is a website or software package

chromosome

updated 10.9 years ago • mehran.karimzade

Hi. If you want to remove reads mapped on a certain chr, how would you do that? I know 'samtools' can extract reads on a chr. Extraction of each chr and combining chr data I want would...problem, but I have multiple bam files to run it. So, if anyone of you know how to REMOVE a single chr (e.g. chr1 only), please tell me. Thank you

RNA-Seq samtools

updated 17 months ago • mbk0asis

I'm still trying to plot some gene features using cytobands as the reference scale. Nevertheless, UCSC and NCBI cytobands don't agree for certain genes...E. g.: human SCN5A is located at 3p22.2 on UCSC Genome Browser. HGNC says it's located at 3p21. NCBI's Entrez Gene agrees with HGNC. Genome coordinates

updated 10.2 years ago • Jarretinha

file I can extract the locus tag and the amino acid sequence however I am struggling to extract the gene location as it not in the same format in the file e.g.: `/locus_tag="NCTC86_00002"` This is my script so far: ```py from Bio import

gbk python gene

updated 15 months ago • kxd419

Hi, I am trying to retrive for a list of genes with their location on the chromosomes: gene_locations<-getBM(attributes = c("ensembl_gene_id","chromosome_name", "start_position...Hi, I am trying to retrive for a list of genes with their location on the chromosomes: gene_locations<-getBM(attributes = c("ensembl_gene_id","chromosome_name", "start_position", "end_position"), filter…

biomart

updated 10.8 years ago • tomislav.ilicic

like to use the `cbind` in a list of files. However each file are split in a specific chromosome (chr) `(k in 1:29)`, and specific sample `(i in 1:777)`. The files are like: sample1chr1.txt, sample1chr2.txt ... sample1chr29.txt, sample2chr1.txt...names). I tried this: #Creating file with row names (3 first columns) to each Chr { {for(k in 1:29){ infile <- paste0("s…

split merge R cbind chr

updated 2.6 years ago • viniciushs88

I'd like to see where PV92 (used in Alu/PCR experiments) is located on the genome (for example: http://www.ncbi.nlm.nih.gov/projects/mapview/maps.cgi?TAXID=9606&CHR=16&MAPS=ideogr

genome chromosome

updated 11.4 years ago • mitchbrk

I have multiple files in format: chr position value. I want to combine them in format "chr", "position", "samp1", "samp2", "samp3", "samp4",........ For example: Samp1: chr position value...I have multiple files in format: chr position value. I want to combine them in format "chr", "position", "samp1", "samp2", "samp3", "samp4",........ For example: Samp1: chr position value 1 377431…

sequencing coverage Assembly

updated 4.5 years ago • Gene

using stringtiemerge with -eB option, I want to do differential expression analysis at the gene level. For that, I tried Ballgown as well as DESeq2 (after getting raw counts using prepDE3). I got the results but my problem...is that I only got gene names or gene ids. Use of either Ballgown or DESeq2 leads to lose of genomic features of the genes such as chr, start, end, strand...to find the corre…

DESeq2 stringtie ballgown RNA-seq

updated 22 months ago • akainth

Dear Friends, I want to download the entire human gene list with the information about their chromosomal location, i.e. that specific gene is present in which chromosome and

genes

updated 10.6 years ago • arulthasan83cyr

Hi, I have a list of Gene Names with mRNA location. I want to know the mRNA Accession no for the particular location in GenBank file. I know it is easy

mRNA miRNA Perl Parsing

updated 6.6 years ago • anshulmbi

Hi, I've been messing around with getting information about mutations at a chromosome location using Ensembl. I currently am loading: my $pf_adaptor = $registry->get_adaptor('human', 'variation', 'phenotypefeature...here][1] it appears dnSNP is a variation type database. Has anyone been able to query dbSNP using chr locations using Ensembl? Thanks [1]: http://useast.ensembl.org/i…

ensembl dbsnp

updated 21 months ago • brady.forcier1

Hello, I am trying to find a tool that I can use to show location of specific genes of interest on a chromosome. Ideally, let say if you want to show where a family of 10 genes appear

chromosome visualization

updated 4.6 years ago • S

Dear all, I need the location of all genes in human which are transcribed by RNA polymerase III. There are some datasets in ucsc/ensembl containing...coordinates of few specific types of pol III transcribed genes (for example tRNA, 7SK RNA). But I could not find anything that covers genes from most of the RNA classes. Any idea how can I

RNA polymerase III human non-coding genes

updated 8.0 years ago • taniasultana2004

naming is just numbered e.g. 1,2,3. I don't know how to change the below code for removing chr instead of adding it? samtools view -h $B | \ sed -e '/^@SQ/s/SN\:/SN\:chr/' -e '/^[^@]/s/\t/\tchr/2' | \ samtools view -bS - > temp.bam Thanks Sara

RNA-Seq

updated 5.4 years ago • jonessara770

I want to compare the expression of a list of genes (mouse) in a specific organ e.g. lung. Also, the chromatin state e.g. which regions are repressed or transcriptionally...I want to compare the expression of a list of genes (mouse) in a specific organ e.g. lung. Also, the chromatin state e.g. which regions are repressed or transcriptionally active...I think MGI gene expression database for gene …

DNA expression chromatin

updated 3.2 years ago • whb

I feel like I'm missing smth very trivial, but how to automatically extract the most complete information on genes chromosomal locations using ENTREZID (preferably in R). I specifically have problems with uncharacterized loci (but sometimes with some genes also). When I use some typical approaches in R I get NA for those loci (e.g. by extracting info from org.Hs.eg.db, v. 3.7.0). For...I'm missin…

R gene

updated 5.0 years ago • aln

I’m looking for a site that has API that allows to search for a gene, and get all domains in that gene based on their gene location, not amino acid location. Is that possible and what is the best

table Pfam Uniprot genome Domain

updated 12 months ago • pickholz.yair

I have a naïve but complex question. I used RSAT to get 5 genes -2000 bp upstream sequence of TSS. I used this FASTA file and binding motif (identified from my experiment) in FIMO to see...motif_id motif_alt_id sequence_name start stop strand score p-value q-value matched_sequence Chr start End Strand 2 D20_ENSG00000130164-LDLR-ENST00000557958 80 108 + 41.9286 1.14E-14 6.18E-10 CTCTGCCACCCAG…

genome

updated 6.5 years ago • kanwarjag

I have a gene expression data set that can be broken down into genes that are significantly differential expressed (DE) after a experimental...condition, and those that are not. I'm interested in knowing if the genes that are significantly DE occur around a subset of chromosomal locations of interest more often that the non significantly...DE genes. I know I have to consider issues of gene length…

gene-clustering Chi-square R Gene-expression

updated 24 months ago • FLDal

my query reads to the genome using bwa. I wish to extract the query sequence that matched with the gene feature. I found column 10 in samtools to provide information on the query sequence that matched to genome (which in many...cases covers outside of gene feature). Since, I am interested in extracting the query base sequence mapped only to the gene feature. Is there a possible...way to perform…

samtools seqkit

updated 10 months ago • L_bioinfo

the fact that I am slightly abusing plotManhattan - I am not trying to plot SNPs but rather entire genes (i.e. start and end positions are different). Here is the data: > head(test) chr start end id pvalue 1 chr2L 10973443 10975293...2178754 FBgn0000097 0.7744837 > str(test) 'data.frame': 10000 obs. of 5 variables: $ chr : chr "…

R software error

updated 8.0 years ago • yotiao

1] from GEO. There is no information about the 'symbol', and I don't know how to convert the ID to gene symbol. The only information I can get are "ID, Chr, Position, GC Score, SNP_ID, SPOT_ID", and the column of "ID" is the same with the...column of "SPOT_ID". The head of the Data table is below: |ID |Chr|Position |GC Score |SNP_ID|SPOT_ID | |GA008510| Y |13311305|0.519…

geo

updated 9 months ago • linhzye

exon-centric splicing analysis using their provided GFF. I would like to convert the chromosome locations they give to gene symbols. Is there a way to do this since biomarts conversion tool is currently unavailable

MISO RNA-Seq rna-seq

updated 8.1 years ago • onspotproductions

number to find it in RefSeq database, I can see features that were annotated, and those are Gene; mRNA; CDS; ncRNA. When I go to it's annotation release, link [here](https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Astyanax_mexicanus...102/), I can see that 25,293 genes are protein coding. Likewise, annotation products are available on ftp site, link [here](https://ftp.ncbi.nlm.nih.gov...gen…

annotation RefSeq coding-genes

updated 2.4 years ago • Ivan

the process of doing enrichment analysis for DEG in Atlantic salmon. To do so, I need to convert the gene names that came out of STAR/HTseq to the same format, so they are uniform. Results sample: ``` # A tibble: 1,053 × 1 id <chr> 1 LOC106612275...1] 191 ``` By looking at the concatenated list of *initial + converted*, there are indeed a few genes that did not g…

biomart R entrez ensembl gene ID

updated 2.3 years ago • Filipe

I am looking at the supplementary material of a study that says there are methylations at location 90752569 of chromosome 10, defined as a S_Shore (UCSC_CpG_Islands_Name=chr10:90750293-90751108) of the FAS gene...they mention its the FAS gene according to UCSC_RefGene_Name.) Under the column Enhancer it says "NA". However, on Genecard this location is not the location...of FAS. Genecard s…

enhancer

updated 2.8 years ago • Shiloh

Hi there, Before I used MEME to search the upstream of genes aiming to look for any motifs. Now, I'm using motifs from MEME and use FIMO to scan through the genome to find whether there...are other locations of these motifs. I got a tsv file from the FIMO, which contains `motif_id | motif_alt_id | sequence_name | star | stop | strand...p-value | q-value | matched_sequence` I was wondering i…

motif FIMO meme

updated 3.6 years ago • Ruixuan

I have the following SNP annotated with variant effect predictor to two genes, their locations in the genome are shown as well (UMD3.1): - rs469441731: chr1:83,591,886-83,591,886 - ENSBTAG00000020106: chr1...I have the following SNP annotated with variant effect predictor to two genes, their locations in the genome are shown as well (UMD3.1): - rs469441731: chr1:83,591,886-83,591,886 - EN…

vep SNP variant effect predictor ensembl

updated 6.7 years ago • serpalma.v

Hi I am a beginner bioinformatic i am searching "how to snp mapping gene?" there are so many R packages for example (i.e, biomaRT, SNPlist .. ) but i have a snplist and gene list I wanna SNPs mapping gene...list using R so i wanna get result file Snp list: Chr POS 1 2 1 3 2 4 2 7 3 5 3 13 4 13 -gene list- Chr start end gene id 1 2 3 a 2 3 5 b …

R SNP gene

updated 5.1 years ago • mmh7272

I am reading a paper which talks about promoter/enhancer regions of certain protein coding genes. These genes are for which evidence points to having strong MEF2 transcription factor binding sites. The paper says...I am reading a paper which talks about promoter/enhancer regions of certain protein coding genes. These genes are for which evidence points to having strong MEF2 transcription factor …

sequence

updated 2.0 years ago • Affan

10510227 G A ##BASE MDD.QC.gz rs ref alt pval effref info chr pos reffrq N rs10 A C 0.9576 -5e-04 1 7 92383888 0.0596 500199 How can I remove the chr:position:allele format in the target

imputation PRSice CHR

updated 3.2 years ago • kstafford32

I am trying to modify the location of features within a GenBank file. I know `feature.type` will give gene/CDS and `feature.qualifiers` will then give...db_xref"/"locus_tag"/"inference" etc. Is there a `feature.` object which will allow me to access the location (eg: `[5240:7267](+)`) directly? This URL give a bit more info, though I can't figure out how to use it for my purpose... http://biopyt…

Genbank python R

updated 2.5 years ago • kavin.pl

of hg38 from gatk or ncbi. All of them are with 'chromosome N' prefix. I need to change it to 'chr' like 'chromosome 1' to 'chr1' . I know hg19 is having chr prefix but in my condition. I can't use hg19

HG38 human reference chr

updated 2.8 years ago • alan

those written and published previously by other authors, I noticed that they can state exactly which genes are located on which chromosomes and which plasmids. However, when I look at my annotation report, I cannot figure out...the locations of some important genes. Can anyone suggest me the software or tools (running on Linux) by which I can run and find such...details about the genes in questio…

genome annotation report

updated 4.8 years ago • El Niño

previously aligned bam files) I have lists of reads (reads name/ID) and their corresponding genomic location (chr and position) where the polyA tail starts, and the estimated tail length for each read. Now I'm would like to see which...gene/transcript each individual read was actually mapped to, which unfortunately isn't provided in the analysis. I am trying...to generate list of chr/position as …

Transcriptomics RNAseq polya

updated 2.2 years ago • joshcylee

I have a list of locations in a bed format chr2 55159107 55160004 chr3 40280597 40282177 chr4 74682484 74683574 chr4 76795449 76796456...10250838 10251741 chr6 20435795 20436466 chr6 31169498 31170294 I am interested to identify genes that are 1000bp (1K) upstream and downstream of each of those location from a gtf file, which belongs to a non model plant

gtf gene

updated 3.9 years ago • aboozar.soorni

34,947 results • Page 2 of 699

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