Metadata for various molecular traits included in the eQTL Catalogue

Metadata for various molecular traits included in the eQTL Catalogue.

The tab-separated files contain the following columns:

• phenotype_id - ID of the molecular trait that has been quantified. This can be either the gene ID (RNA-eq eQTLs), probe ID (microarray eQTLs), transcript ID (full-length transcript usage QTLs), splice junction ID (Leafcutter), exon id (exon-level QTLs) or any other molecular trait that has been quantified.
• quant_id - Used to quantify relative transcript usage or relative transcriptional event usage (in txrevise). 
• group_id - Used for transcript usage and splicing phenotypes. Overlapping phenotypes whose relative expression is quantified belong to the same group (e.g. alternative spliced exons form clusters in Leafcutter). QTLTools permutation p-values are calculated accross all phenotypes within a group and only the phenotype with the smallest permutation p-value is reported.
• gene_id - Ensembl gene id
• chromosome - Chromosome of the gene
• gene_start - End coordinate of the gene (GRCh38)
• gene_end - Start coordinate of the gene (GRCh38)
• strand - Strand of the gene
• gene_name - Gene name extracted from Ensembl biomart.
• gene_type - Gene type extracted from Ensembl biomart.
• gene_gc_content - Percentage GC content of the gene. Extracted from Ensembl biomart and used as a covariate in cqn normalisation. Calculated with bedtools nuc for exons.
• gene_version - Ensembl gene version
• phenotype_pos - Genomic position used to determine the centre point of the cis-window for QTL mapping. By default this is the beginning of the gene (either gene start or gene end, depending on the strand of the gene).
• phenotype_length - (optional) - Length of the gene or exon in basepairs. Required to properly normalise featureCounts quantification results with cqn.