e4e3a81fd04f0a799894b069d1977092d60f5bba jnavarr5 Thu Aug 7 15:43:08 2025 -0700 Updating the track description page. Moving the Methods section before the Data Access, restructuring the Display Conventions section, adding a link to the recount3 website... Removing .html from the html line in trackDb, refs #34886 diff --git src/hg/makeDb/trackDb/recount3.html src/hg/makeDb/trackDb/recount3.html index 481ad806789..a1b0ba6c578 100644 --- src/hg/makeDb/trackDb/recount3.html +++ src/hg/makeDb/trackDb/recount3.html @@ -1,81 +1,84 @@

Description

-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. +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.

Display Conventions

-Intron blocks are grayscale colored based on read support (darker tones indicate higher coverage).
-Split read counts and splice motifs are shown on mouseover.
+Intron blocks are grayscale colored based on read support (darker tones indicate higher coverage). 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 ends are color coded: +on the track configuration page. The SRA track is only visible when zoomed in within 10 million +bases because of its data density. +

+

+The intron ends are color-coded:

-Introns with non standard ends do not have colored tags. -
-The SRA track is only visible when zoomed in within 10 million bases because of its data density. +

+Split read counts and splice motifs are shown on mouseover. +

+ +

Methods

+

+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.

Data Access

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 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)

-

Methods

-

-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. -

-

References

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