• Bulk download introns, exons, and UTR regions from Ensembl for gene prediction training set

    Hi, I would like to download labeled FASTA sequences of introns, exons, 5' UTR regions, and 3' UT...

  • How to download all premRNA sequences (exons + introns) for human GRCh38 with Ensembl IDs?

    I'm not seeing anything on the FTP website that has this info:
    ftp.ensembl.org/pub/release-...

  • Should cndas provided by Ensembl be filtered by ccds or biotype prior to running kallisto?

    I typically download cdnas directly from Ensembl (like with `wget ftp.ensembl.org/pub/relea...

  • Get Exons & Introns Using Ensembl Rest Api

    Hello all

    I have some gene IDs from Ensembl and I want to get their transcripts' exons and intro...

  • Searching a DNA sequence for eukaryotic genes

    How to find eukaryotic genes from [this][1] FASTA format of a sequence in human chromosome 13?

    ...

  • How to download an unspliced transcript for a given Ensembl ID using the perl API

    This is the code snippet I have so far:

    my $gene_adaptor = $registry->get_adaptor( 'Human...

  • Ensembl Exon Order

    Hi to everyone. I have a question about Ensembl Exon Order.

    Specifically:

    I have used Biomart t...

  • Difference Between Biomart Query And The Ensembl Database

    Hi,

    I'm using the biomaRt R packages (bioconductor) to retrieve the 3'UTR sequences of a list of...

  • How to download all transcripts from Mouse with exons as upper case and introns as lower case?

    I was using UCSC's Table Browser before but you have to input the transcript IDs and most of the ...

  • How To Download All The Introns From Ensembl

    Hi,

    I would like to know how could I download all the introns (in FASTA) of a species from Ensem...

  • Understanding the gffcompare output for my dataset

    Hi all,
    Below is the output from gffcompare of assembled transcripts from my RNA-seq experiment w...

  • Sending multiple REST commands over the same URL connection

    Hello,

    I am using Ensemble REST API to retrieve genomic coordinates based on positions in CDNA t...

  • Question about getSequence function of biomaRt in R

    Hi everyone,

    I am working on a project about copy number variant calling algorithms. One questio...

  • Mapping between gene IDs and transcripts IDs in C. elegans

    Dear Community,

    I am looking to build a mapping file between the gene names of C. elegans and it...

  • cuffcompare: No novel genes found. Is this possible?

    I tried to run cuffcompare using cufflink assembled transcript output and an annotation file. I w...

  • Several exonerate options; which to choose?

    I am wanting to identify exon-intron boundaries between transcripts and a genome for a given spec...

  • Defining exons, UTRs, introns and intergenic regions using "overlap" in Ensemble REST API

    Hi all!

    I want to define whether a region with given coordinates overlaps with intron or exon ...

  • How to make an intronic GTF for alignment

    Hi,

    I was struggling to find an intronic GTF for some RNA-seq alignment. Several page showed how...

  • Where To Download Hg19 Gene Annotation, Transcript Annotation And Cdna Fasta Files?

    Hi, I am hanging around to look for hg19 transcript annotations together with cDNA fasta files.
    ...



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