1b34ddd99f21b5b31c9c0b65ed7957fe29d29fb9 markd Tue Aug 19 10:21:11 2025 -0700 updates to recount3 tracks (not complete) diff --git src/hg/makeDb/trackDb/recount3.html src/hg/makeDb/trackDb/recount3.html index a1b0ba6c578..dc46a70417a 100644 --- src/hg/makeDb/trackDb/recount3.html +++ src/hg/makeDb/trackDb/recount3.html @@ -1,84 +1,95 @@

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. -

-These tracks display the recount3 intron data including split read counts. +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.

Display Conventions

-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 SRA track is only visible when zoomed in within 10 million -bases because of its data density. +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 ends are color-coded: +The intron items are color-coded:

Dark blue GT donors and AG acceptors (CT and AC on +
Blue GT donors and AG acceptors (CT and AC on the minus strand)
Teal GC donors (GT on the minus strand)
Faded red AT donors and AC acceptors (GT and GT on the +
Turquoise GC donors (GT on the minus strand)
Orange AT donors and AC acceptors (GT and GT on the minus strand)
Introns with non-standard ends do not have colored tags.
Grey Non-canonical junction motifs. These could be sequencing errors, polymorphisms, or very rare U12 introns.

-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. +Introns can be filtered by: +

read count - Number of split reads supporting the intron. The default is a minimum of 10,000 reads.
intron size - Length of the intron. The default is 30 to 100,000.
splice junction motif - The motif is specified in the form GT/AG, with canonical motifs being uppercase and unknown motifs being lowercase. + The default is no filtering.
strand - Filter by positive strand ('+'), + negative strand ('-'), and/or + unknown strand ('.'). The default is no strand filtering ('all'). +

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