Annotation for the genome in the boundle

Hi,

I did a RNA-seq GATK analysis with a genome supplied in the bundle - human_g1k_v37_decoy.fasta. I would like to find corresponding annotation to this genome, which is not supplied in the bundle. Which annotation would you recommend to use?

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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    What kind of annotation are you looking for?
  • oleagaoleaga NorwayMember

    A gene annotation, a gtf or gff file.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    That's not something we provide, but you should be able to find one via eg this Biostars thread.

  • oleagaoleaga NorwayMember

    Well, to be more specific, I was wondering which version of the GRCh assembly annotation should I use? Which version of the assembly human_g1k_v37_decoy is based on? Thank you!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Ah, that's a good question -- to be frank I don't know and I'm not sure who would. My understanding is that any of the gene annotation files should be compatible with the primary sequence as long as it's the correct build (here, b37). The nucleotide sequence and contig lengths are supposed to be guaranteed to remain the same, iirc.

    @shlee Would you have any insight into this?

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