get CDS cordinates for genes, excluding UTR

Hi all,

I want to collect the gene exon cordinates information for GATK variant calling usage.

As far as I know, UCSC can offer me the great utility to extract the information.

Howver, it can only extract exon only or UTR only.

Although I can write a script to get those cordinates and find the real CDS regions excluding UTR, is there any tool or website can extract such bed information?

Thanks,

Junfeng

cds gene

• 1,510 views • link

written 8.7 years ago by J.F.Jiang

0 answers

No answers yet.

More posts like this

Reference panel of normals for ensembl named refgenome
written 2.2 years ago by gernophil •

Hey everyone, I am doing a lot of variant calling. So far, I have always used the Ensembl refgenomes with the "number only" nomenclature for …
Gffread_How to obtain fasta files of gene features (ORF, UTR) by transcripts based on gff?
written 6.2 years ago by tianshenbio

I have a gff like this: Bany_Scaf24 maker gene 41357 46444 . + . ID=Bany_09696;Name=Bany_09696;Alias=maker-Bany_Scaf24-exonerate_est2genome-gene-0.0; Bany_Scaf24 maker mRNA 41357 46444 . + . ID=Bany_09696-RA;Parent=Bany_09696;Name=Bany_09696-RA;Alias=maker-Bany_Scaf24-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_QI=277|1|1|1|0|0|2|35|76;_eAED=0.00;score=1829; Bany_Scaf24 …
Tool: AGAT - Another Gff/Gtf Analysis Toolkit
written 6.6 years ago by Juke34

# **[AGAT][1]** - Another Gff/Gtf Analysis Toolkit Suite of tools to handle gene annotations in any GTF/GFF format. Available through conda and Docker for an …
Extracting sequence and annotation of a particular gene
written 7.4 years ago by Adrian Pelin

Hello, I have the human and mouse GENCODE annotations and the genome that goes with it. I am interested to create sequence and annotation files …
Using UCSC Genome Browser with results from NCBI or Ensembl assemblies
written 8.6 years ago by colin.kern

If I want to display some data on the UCSC genome browser, but have done the analysis with the Ensembl or NCBI assemblies and annotations, …
Extracting 5'UTR and 3'UTR bed files from gtf file
written 8.7 years ago by c_u

Hi, I have the gtf file for mouse, and I wanted to create bed files for the 5' and 3' UTRs using this gtf file …
How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
written 11.6 years ago by A. Domingues

I am trying to do differential gene expression analysis, and analysis of 3'UTR usage, in a knock-down experiment in Zebrafish (RNA-seq, PE). Since I am …
How to get all the versions of refSeq
written 12.0 years ago by talmud.k •

I have downloaded some databases to make an annotation of my sequencing results. But I found that sometimes there is only the HGVS description of …
Phased And Imputed Genotypes For Hapmap Samples With Plink Format
written 13.0 years ago by J.F.Jiang

Hi all, I am looking for the phased and imputed genotypes for hapmap samples with plink format. Although I can download the raw genotypes from …
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
written 13.0 years ago by J.F.Jiang

Hi all, I want to extract the genomic region of 3'UTR and 5'UTR from the GENCODE gtf annotation file to make a bed file for …