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.
These tracks display the recount3 intron data, including split read counts and splice junction motifs.
Intron items are colored based on splice junction motifs and read support (darker colors indicate higher 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 setting can be changed on the track configuration page.
The intron items are color-coded:
Introns can be filtered by:
The original junction files can be found at
https://snaptron.cs.jhu.edu/data/gtexv2/junctions.bgz
https://snaptron.cs.jhu.edu/data/tcgav2/junctions.bgz
https://snaptron.cs.jhu.edu/data/srav3h/junctions.bgz
https://snaptron.cs.jhu.edu/data/ccle/junctions.bgz
https://snaptron.cs.jhu.edu/data/srav1m/junctions.bgz (mouse)
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.
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