• split a GFF3 with many Genomes to GFF3 files with individual Genomes

    Hi all,
    I have a big GFF3 file that I downloaded from Batch Entrez and it contains 54 genomes. I ...

  • should stop codon be counted as part of CDS

    I am analyzing the GTF file at ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/Homo_sapien...

  • 'CDS' but not 'exon' in GFF

    Hi,

    I'm working with RNAseq data from *A. thaliana*. Reads were mapped with STAR 2.6 using the ...

  • Multiple CDS of a same gene

    Hi,
    I have googled a lot about this query but I could not find a suitable answer.

    I downloaded s...

  • Need some clarifications in snpEFF annotation in extracting exonic variants

    Hi All,

    I have generated single vcf for 2 samples. Then annotated the vcf file using snpEff and ...

  • Convert gff3 to gtf with R or shell

    Hi,

    I have gff3 file in the following format:

    #gff-version 3
    ##sequence-region Chromo...

  • generating 'maximal' cds sequence from multiple isoforms of a gene

    For a given gene, I would like to take the exons or CDS coordinates for all isoforms and 'merge' ...

  • NCBI, Gene, Exon count

    Hello
    I want to find the exact number of my genes exons. I have 2 genes: NKX2-5 and GATA4
    I know ...

  • Exons in Refseq-hg19

    Hi,

    I was working with the refseq genes hg19 file to define genomic regions and I downloaded 4 f...

  • Ensembl CDS anomalies

    I am looking for a FASTA file of all CDS in the mouse genome.

    The Ensembl  website claims to hav...

  • Why two gene sequences are different beetween ensembl and ncbi?

    Hi, I need to get a DNA (no mRNA) sequence of that gene: www.ncbi.nlm.nih.gov/gene/6271
    A...

  • infer 3' and 5' UTR from gff3 file

    Hi,
    I have a gff3 file wtih info: CDS exon intron and parent genes.

    I am interesting to define ...

  • Can gffread extract specific region sequences from vcf or fasta file?

    Hello, I have NGS sequencs result(vcf and fasta) file, I download reference sequence([GFF3 format...

  • Criteria for denoting unknown data in cosmic db

    I am wondering the criteria for denoting unknown data in cosmic db.

    for example PIK3CA gene,

    ...

  • How to take exon sequence of a gene for multiple species??

    I need to take exon sequence of MSTN gene of myotis davidii and then compare it with various spec...

  • augustus output - how is the incompatible hint groups determined?

    Hi, I have a question about the augustus (v3.0.2, v3.0.1) output - specifically when it reports t...

  • Why is the cds start and cds end position the same in some of the known-gene data downloaded from ucsc ? (ucsc table browser)

    I am working on human cancer data and wanted to extract sequences from the human genome for analy...

  • Salmon: Optimal k-mer size (for indexing) for RNA-seq data alignment using reference genome

    Dear all,

    I am using [salmon][1] to evaluate how the L.donovani gene expression varies in the t...



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