I have a list of 54000 gene-ids I want to annotate all the genes. Is there any other R package or command-line software that I can use?
your question is very vague!
Can you elaborate on what exactly you want to achieve? since you already have a gene number I assume it's functional annotation you're looking for?
Sorry for the vagueness. U are right, I want to annotate the genes. I m trying to use geneSCF for the same as it is command-line based but I have NM and NR ids becoz of which it is giving errors. So kindly guide further. Is there any other command-line based annotation tool or any R package for the same.
So these are Refseq ID. What do you want to do with the annotation and which species they belong to? geneSCG is clustering them based on functional relevance but these are too many ids, probably the entire transcriptome. Tell specifically the aim of the design and what you want to perform.
What I used:
But simply searching in google scholar will give you tons of papers where people did this in different ways. You can also homebrew it yourself, building blast databases and blasting sequences against them.
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