Hi, Could you post the Ensembl Gene to Gene Symbol mappings of the genes you used in your RNAseq data files? I downloaded these mappings from Ensembl BioMart today, however many Ensembl Gene ids used in RNAseq files are missing. (Btw, are Ensembl gene IDs getting updated so frequently??) Eventually, I want to get the RNA level expressions of the TFs from the supplied RNAseq data. Thanks a lot! Biter

Created by Biter Bilen biterbilen
Hi Biter, You can use the GENCODEv19 annotations http://www.gencodegenes.org/releases/19.html that we pointed to in the Gene Expression section of the Accessing Data page on the Synapse wiki https://www.synapse.org/#!Synapse:syn6131484/wiki/402043 Specifically this GTF file ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/gencode.v19.chr_patch_hapl_scaff.annotation.gtf.gz has ENSEMBL IDs and gene names associated with each entry. If you are unable to associate them using the GENCODE annotations, please paste the list of ENSEMBL IDs you are unable to associate to gene names and we can check if there are any issues. Thanks, Anshul.

Ensembl Gene Ids in RNAseq data are missing in Ensembl BioMart downloaded mappings page is loading…