I noticed recently that when converting a list of 46,676 MGI annotated genes to mm10 ENSEMBL annotation using bioMart, about 8,000 genes included in the original dataset are omitted from conversion.
Some of the genes omitted from the conversion, such as Zcchc6 and Zcchc11 are definitely annotated on ENSEMBL(ENSMUSG00000034610 and ENSMUSG00000035248 respectively), so I was wondergin why that could be.
I tried updating bioconductor but this did not improve the situation.
I was thinking of trying the ENSEMBL perl API next but was wondering if anyone else had experienced a similar problem with bioMart? What is the solution to this problem?
Thanks in advance for your help.