How do I figure out what annotation package to use with a transcriptome?
I have reads counted with rna.fa.gz from:
I can't find an NCBI annotation package for Mm, or any Mm annotation package that references build 37.
Names look like this:
 "gi|126352347|ref|NM_028260.2|" "gi|142348699|ref|NM_010886.2|"
 "gi|23821034|ref|NM_017376.2|" "gi|33239323|ref|NM_146675.1|"
 "gi|118130860|ref|NM_133839.2|" "gi|29789242|ref|NM_024451.1|"
I thought that the numbers following 'gi|' would be entrez gene identifiers.
So I tried org.Mm.eg.db. But this doesn't seem to work:
> x <- org.Mm.egGENENAME
> mapped_genes <- mappedkeys(x)
I'm confused and don't know what to try.