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• 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 http://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: https://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...