I am getting problems when trying to convert refseq_rna ids (for example, NM_001300384.1) to flybase_gene_id using biomaRt (in R and online), despite the fact that when I put this rna id to ensembl it gives me the right record (http://www.ensembl.org/Multi/Search/Results?q=NM_001300384.1;site=ensembl) (ensembl is using the same gene and transcript ids as FlyBase).
> library(biomaRt) > ensembl<-useMart("ensembl", dataset="dmelanogaster_gene_ensembl") > getBM(attributes="flybase_gene_id", filters="refseq_mrna", values="NM_001300384.1", mart=ensembl)  flybase_gene_id <0 rows> (or 0-length row.names)
This is a part of my analysis where I annotate probes by local blast (which only produces NCBI accession numbers) and convert them to ensembl gene ids. But I am stuck at this conversion and don't understand what's going on. I also note that if I have several transcripts/transcript variants each with a different NCBI ID, the shortest ID (i.e. with fewest digits) usually gives me a hit in biomaRt. But long IDs like the above (of which I have many thousands) don't work.
I would very appreciate the explanation for this behaviour and tips on how to get the conversion done.