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sagnikbanerjee15 / Finder

A fully automated gene annotator from RNA-Seq expression data
MIT License
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Protein FASTA from closely related species #29

Open saxovocal opened 2 years ago

saxovocal commented 2 years ago

Thank you for the wonderful package.

I have plenty of transcriptome data for my species, but I do not have a protein fasta. Is it recommended to use a protein fasta from a closely related species?

I read your paper's section on "De novo gene prediction from expression data and proteins from closely related species" but am unsure whether this meant using both short read data and protein level data, or both.

sagnikbanerjee15 commented 2 years ago

Hello @saxovocal,

Thank you for your interest in finder. It is very generous of you to call it wonderful!!

Protein sequences are additional information that would supplement the gene models constructed from RNA-Seq data. If you have sufficient RNA-Seq data then you do not require any protein sequences.

Please let us know if you encounter any issues while executing finder.

Thank you.