How are transcriptome annotations published?
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2 days ago
Dunois ▴ 600

I see plenty of papers describing annotations of de novo assembled transcriptomes, but I can't really seem to put a finger on the accepted method of publishing an annotated transcriptome.

For instance, this paper uploaded their data to figshare. But this paper only mentions a BioProject ID.

So my questions:

  • How does one publish an annotation of a transcriptome?
  • Is there any criteria on what files need to be uploaded? I presume a FASTA with the sequences and a table of some sort relating the headers to human-readable annotations would be the bare minimum. Or is a FASTA file with human-readable headers sufficient? Is some sort of a "raw" assembly FASTA file also necessary?
  • What else can one publish as a part of a transcriptome annotation?
  • What platforms are considered suitable for publishing the annotation data? GitHub? figshare?

Your inputs would be much appreciated.

RNAseq annotation publish transcriptome • 146 views
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Do you only have transcriptome annotation with no genome sequence? If you do you may be able to use Eukaryotic genome annotation submission method for GenBank. You can also email NCBI support and ask them about options.

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Thanks for the links to the papers/repos. Wouldn't it be enough to upload a .fasta, ORFs and annotation in .gff3? Good luck!

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I don't know, that's why I'm asking. Like what do you do if you're transferring annotations off of multiple resources?

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