21Mar

Extract last exon annotation from each mRNA

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  • Splice donor site mutation

    I am having a missense mutation at the last base of exon i.e. exon 13 of a gene having 15 coding ...

  • How To Retrieve Mrna Split Locations From Genbank Flatfile?

    Hi all,

    I got some trouble parsing the genbank flatfile format that ncbi is using for data expor...

  • HISAT2 index creation

    Dear all,
    I am trying to create index file using the splice site and exon information from the .g...

  • Extracting Intron-Exon Reads from bam files

    I would like to extract intron-exon reads (unspliced reads) from bam file. I tried use the with ...

  • Need Help with splicing exons on Python

    When mRNA is transcribed from the chromosome, it briefly includes not only the exons with the pro...

  • Getting Genome Coordinates From Refseq Exon Mrna Position Data?

    I am using bioperl to obtain exon coordinates for a variety of mRNAs.... For example:

    #!/usr/bi...

  • How to extract coordinates of first exons from .gtf file.

    Hi All, 

     

    Supposed I have a .gtf file with the exons of all genes in a given genome. I would l...

  • How to extract the last 1000 nt from a group of sequences in a FASTA file?

    Hi everyone!

    I would like to know how I can extract the 1000 last nucleotides from sequence in a...

  • Extract gene sequences from gff3 file and reference fasta

    Hi,

    I have a gff3 file and I want to extract the gene sequences (not including introns). Several...

  • Alternative splicing event annotations method

    Hi,

    I am looking for a computational method to identify the number of instances of each alternat...

  • How To Resolve The Gene To Mrnas Relationships For The Human Genome?

    I'm interested in analyzing gene and mRNA annotations for the human genome. In addition to the ex...

  • How to filter "only Mrna "s from total RNA ?

    Hi everyone,

    I am working with a data set of total rna. Already extracted a list of Biomart fro...

  • Extracting Statistically Significant Differentially Expressed Exons From Dexseq Results

    Hi

    I am trying to extract some data from my DEXseq results. I was able to get the final HTML rep...

  • Calculation of read counts in RNA-seq

    Hi everybody,

    I'm reading the steps of generation of read counts in an RNA-seq study which are a...

  • How to extract exon sequences from annotated genome

    I have a .gff3 file for an insect genome, which looks like the following:

    > Scaffold1 I5K...

  • How to extract reads belonging to sense intron/exon and antisense intron/exon while working with small RNA sequence

    I have Illumina data of 1 x50bp from small RNA library. I am interested in identifying known and ...

  • Extracting the coding sequences for a set of protein IDs - NCBI.

    I have a set of protein IDs. In reality there are thousands, but for this example, there are thes...

  • How to get Cufflinks data for MISO alternative splicing events?

    Hello,

    i am currently doing an analysis on splice junctions at alternative exons, that belong to...

  • Average length of each exon and intron

    Hi,

    I want to estimate the average length of each exon and intron (first 3 and last 3) from the...

  • Extracting the donor/acceptor sites from mRNA sequence(PERL/ DNA transcription) ?

    I have the following program that I am analyzing and trying to understand. Overall purpose of ...

  • A question about splicing

    Hello,

    I have a question I hope that someone here will be able to answer.

    Its concerned with R...



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