Metadata for various molecular traits included in the eQTL Catalogue

Metadata for various molecular traits included in the eQTL Catalogue. 

Metadata files for the Leafcutter datasets can be found here.

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.