New recount3 track for hg38 and mm10

[Gerardo Perez]

Hello Everyone,

We are happy to announce the release of the recount3 track for hg38 and mm10. 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.

The tracks display recount3 intron data, including split read counts and splice junction motifs.

For hg38, the tracks available are:

• recount3 GTEx introns
• recount3 TCGA introns
• recount3 SRA introns
• recount3 CCLE introns

For mm10:

• recount3 SRA introns

Introns can be filtered by intron size, split read count, splice junction motif, and strand; intron items are color-coded, with darker colors indicating higher coverage:

• Sky blue: GT donors and AG acceptors (CT and AC on the minus strand)
• Turquoise: GC donors and AG acceptors (CT and GC on the minus strand)
• Orange: AT donors and AC acceptors (GT and AT on the minus strand)
• Grey: Non-canonical junction motifs. These could be sequencing errors, polymorphisms, or very rare U12 introns.

We would like to thank the ReCount team for making this data available. We would also like to thank Jeltje van Baren, Mark Diekhans, and Gerardo Perez for their efforts on this release.