where do I find transcript_biotype

Question

[newbie_r]

I am trying to fetch gene_biotype and transcript_biotype from the NCBI ftp site (link: https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/latest_assembly_versions/GCF_000001405.39_GRCh38.p13/)

I was able to get gene_biotype from GCF_000001405.39_GRCh38.p13_genomic.gff.gz from the above link.

However, I couldn't find transcript_biotypes. Where do I fetch the transcript biotypes?

Thanks and regards R

Answer 1

[Kevin Blighe]

Hi newbie_r,

I am unsure; however, via biomaRt in R, one can generate a master table that has biotypes for Ensembl and RefSeq 'transcripts'.

require(biomaRt)
ensembl <- useMart('ensembl', dataset = 'hsapiens_gene_ensembl')

annot <- getBM(
  attributes = c(
    'hgnc_symbol',
    'ensembl_gene_id',
    'ensembl_transcript_id',
    'entrezgene_id',
    'refseq_mrna',
    'gene_biotype'),
  mart = ensembl)

head(subset(annot, refseq_mrna != ''))
   hgnc_symbol ensembl_gene_id ensembl_transcript_id entrezgene_id  refseq_mrna
45       INTS3 ENSG00000262826       ENST00000576030         65123    NM_023015
46       INTS3 ENSG00000262826       ENST00000576030         65123 NM_001324475
62     KIR2DL3 ENSG00000273947       ENST00000616520          3804    NM_015868
66     KIR2DL4 ENSG00000276779       ENST00000618567          3805 NM_001080770
67     KIR2DL4 ENSG00000276779       ENST00000618567          3805    NM_002255
75     KIR3DL2 ENSG00000273735       ENST00000620501          3812    NM_006737
     gene_biotype
45 protein_coding
46 protein_coding
62 protein_coding
66 protein_coding
67 protein_coding
75 protein_coding

There is also the attribute refseq_ncrna that can be used.

Kevin

Answer 2

[Congcong]

The gene_biotype info is documented at the ninth column in gtf file. you can extract conveniently those info using the stringr package