8e2ce67692e814db90b2d2938915712ff9b0ee51 jeltje.van.baren Wed Apr 16 18:07:03 2025 -0700 Adding recount3 #34886 diff --git src/hg/makeDb/trackDb/recount3.html src/hg/makeDb/trackDb/recount3.html new file mode 100644 index 00000000000..1dfccbf8870 --- /dev/null +++ src/hg/makeDb/trackDb/recount3.html @@ -0,0 +1,81 @@ + + + + + + +

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. +

+ + +

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.
+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: +

+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. +

+ +

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.tgz
+ +https://snaptron.cs.jhu.edu/data/tcgav2/junctions.tgz
+ +https://snaptron.cs.jhu.edu/data/srav3h/junctions.tgz
+ +https://snaptron.cs.jhu.edu/data/ccle/junctions.tgz
+ +https://snaptron.cs.jhu.edu/data/srav1m/junctions.tgz (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 +