Recount3 is a comprehensive resource for re-analyzing RNA-seq data. It provides uniformly processed RNA-seq data and associated metadata from a wide range of studies, enabling researchers to access and analyze gene expression data in a consistent manner. Recount3 aggregates data from multiple sources, including the Sequence Read Archive (SRA) and the Genotype-Tissue Expression (GTEx) project, and reprocesses it using a standardized pipeline. This allows for cross-study comparisons and meta-analyses, facilitating discoveries in genomics and transcriptomics. Processed recount3 data were integrated into the Snaptron system for indexing and querying data summaries. Recount3 is available at: http://rna.recount.bio.
These tracks display the recount3 intron data, including split read counts and splice junction motifs. For hg38, tracks are available for GTEx, TCGA, SRA, and CCLE data sources, while mm10 includes the SRA track only.
Intron items are colored based on splice junction motifs and read support. Darker colors indicate higher read coverage. Split read counts and splice motifs are shown on mouseover. By default, only introns with a minimum read count of 10,000 are shown. This threshold can be changed on the track configuration page.
The intron items are color-coded (darker colors indicate higher coverage):
Introns can be filtered by:
A distributed processing system for RNA-seq data called Monorail was developed. Using Monorail, recount3 processed and summarized 316,443 human and 416,803 mouse RNA-seq run accessions collected from the Sequence Read Archive (SRA), with the human runs including large-scale consortia such as GTEx v8 and The Cancer Genome Atlas (TCGA).
Junction files were converted to BED format. For grayscaling total read count was log10 transformed and multiplied by 10 to get a score between 0 and 225, which can be found in the BED score field.
The raw data can be explored interactively with the Table Browser or the Data Integrator. For automated analysis, the data may be queried from our REST API.
Please refer to our mailing list archives for questions or our Data Access FAQ for more information.
The original junction files for human can be found at:
The mouse junction file is available at:
Wilks C, Zheng SC, Chen FY, Charles R, Solomon B, Ling JP, Imada EL, Zhang D, Joseph L, Leek JT et al. recount3: summaries and queries for large-scale RNA-seq expression and splicing. Genome Biol. 2021 Nov 29;22(1):323. PMID: 34844637; PMC: PMC8628444