Ruminantia

Expression Atlas

RNA-Seq Pipeline

The raw RNA-Seq reads were pre-processed to remove adapters and low quality bases using Trimmomatic. The remaining high-quality reads were aligned to the corresponding reference genome using STAR and HISAT2. Then StringTie was used to assemble the alignments into full and partial transcripts. Fragments per Kilobase per Million mapped reads (FPKM) values for each genes were calculated by using Ballgown.

RNA-Seq Collections

The expression atlas database includes 1232 RNA-seq datasets (goat: 131, sheep: 832, cattle: 163, yak: 27, water buffalo: 39, roe deer: 20, and sika deer: 20).
Click on the related species to search gene expression in heatmap and Genome Browser.