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, +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. +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.
-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. +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: +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.
+REST API.
Please refer to our mailing list archives -for questions, or our +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 at: +The mouse junction file is available at:
- - --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