Dear All,

I have Illumina array probe metadata with me HumanHT-12_V3_0_R3_11283641_A.txt. Now, I need to annotate the gene symbols present within them. Precisely, I need to know the biotype of all genes available in the Illumina metadata file. The file consists of 48k genes. When I use GENCODE GTF file (hg38). I can annotate 24k genes, and the rest is not annotated. In that case, I would like to know, whether there is any annotation file specific for Illumina? The HEADER of the above-mentioned file consists of,

? Illumina, Inc.
[Heading]
Date    7/1/2010
ContentVersion  3.0
FormatVersion   1.0.0
Number of Probes    48803
Number of Controls  784
[Probes]
Species Source  Search_Key  Transcript  ILMN_Gene   Source_Reference_ID RefSeq_ID   Unigene_ID  Entrez_Gene_ID  GI  Accession   Symbol  Protein_Product Probe_Id    Array_Address_Id    Probe_Type  Probe_Start Probe_Sequence  Chromosome  Probe_Chr_Orientation   Probe_Coordinates   Cytoband    Definition  Ontology_Component  Ontology_Process    Ontology_Function   Synonyms    Obsolete_Probe_Id

Currently, I extracted the ILMN_Gene and tried to annotate it with the GENCODE GTF file. However, I am not able to get the biotype of all genes within the Illumina file (48k).

Any suggestions would be of great help Thanks!