recount3: uniformly processed RNA-seq


recount3 is an online resource consisting of RNA-seq gene, exon, and exon-exon junction counts as well as coverage bigWig files for 8,679 and 10,088 different studies for human and mouse respectively. It is the third generation of the ReCount project and part of recount.bio.

The raw sequencing data were processed with the Monorail system as described in the recount3 paper which created the coverage bigWig files and the recount-unified text files. While these raw output files are available through IDIES SciServer, for ease of statistical analysis, we provide through the recount3 R/Bioconductor package an interface that builds RangedSummarizedExperiment R objects for gene, exon, and exon-exon junction counts for each study. Furthermore, snapcount enables query-based access of the recount3 and recount2 data. The coverage bigWig files can be used for annotation-agnostic expression analyses using for example megadepth, derfinder and other tools.

By taking care of several pre-processing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward. For more details about recount3, check the documentation book.

Study explorer

You can open the study explorer independently through shinyapps.io to explore the data hosted by the recount3 project.

recount3: uniformly processed RNA-seq


recount3 is an online resource consisting of RNA-seq gene, exon, and exon-exon junction counts as well as coverage bigWig files for 8,679 and 10,088 different studies for human and mouse respectively. It is the third generation of the ReCount project and part of recount.bio.

The raw sequencing data were processed with the Monorail system as described in the recount3 paper which created the coverage bigWig files and the recount-unified text files. While these raw output files are available through IDIES SciServer, for ease of statistical analysis, we provide through the recount3 R/Bioconductor package an interface that builds RangedSummarizedExperiment R objects for gene, exon, and exon-exon junction counts for each study. Furthermore, snapcount enables query-based access of the recount3 and recount2 data. The coverage bigWig files can be used for annotation-agnostic expression analyses using for example megadepth, derfinder and other tools.

By taking care of several pre-processing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward. For more details about recount3, check the documentation book.

Study explorer

You can open the study explorer independently through shinyapps.io to explore the data hosted by the recount3 project.