[genome-announce] New GTEx cis-eQTL and RNA-seq read coverage tracks for human (hg38)

[Jairo Navarro Gonzalez]

Hello everyone,

We are happy to announce the release of two new tracks for the human assembly (GRCh38/hg38): the GTEx High-Confidence cis-eQTLs from CAVIAR and GTEx RNA-seq read coverage tracks.

GTEx High-Confidence cis-eQTLs from CAVIAR

• Shows genetic variants likely affecting proximal gene expression in 49 human tissues from the Genotype-Tissue Expression (GTEx) V8 data release.
• Items in the track are colored according to their tissue, with the color matching those in the GTEx Gene V8 Track.
• The data items displayed are gene expression quantitative trait loci within 1MB of gene transcription start sites (cis-eQTLs), significantly associated with gene expression and in the credible set of variants for the gene at a high confidence level, with a causal posterior probability of >0.1.
• Raw data for these analyses are available from the GTEx Portal.

GTEx V8 RNA-Seq Read Coverage by Tissue

• The NIH Genotype-Tissue Expression (GTEx) project determined genetic variation and gene expression in 52 tissues and 2 cell lines using RNA-seq data (V8, August 2019), on 17,382 samples from 948 adults.
• This track focuses on gene expression and shows read coverage, from one single sample per tissue, selected for high-quality and high read depth. The data is summarized to one number per base pair, the number of sequencing reads that cover this position.
• The plot shows if a given exon is transcribed primarily in certain tissues and whether transcription is uniform over the length of a single exon.
• Data can also be obtained directly from the GTEx Portal.

We would like to thank the GTEx investigators, analysts, and portal team for providing this data. 

Jairo Navarro 
UCSC Genome Browser
UC Santa Cruz Genomics Institute
Revealing life’s code. Google Scholar | Twitter | Facebook | YouTube