Hi, I am trying to replicate the eQTL results using MatrixEQTL in R. The MatrixEQTL requires gene position as input for identifying cis. I found there is no such information in the gene expression file. When I try to recover the gene position by matching the ENSG ID of gene expression (synapse ID syn5607698) with those in the 'CMC_MSSM-Penn-Pitt_DLPFC_mRNA_IlluminaHiSeq2500_Ensembl70TranscriptMetadata.txt' file (synapse ID syn5602138), I found some of the ENSG IDs are not found in this Metadata. I wonder what is the reference used in annotating the gene positions? Thanks.

Created by Jin Liu gordonliu810822
Thank you for your reply
Hi Jin- The reference used was Ensembl 70. The file you linked to is a transcript annotation file for the MISO transcript analysis, which is why not all genes are present. Solly

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