< recount3 | Recount3 is a comprehensive resource for re-analyzing RNA-seq data. It provides uniformly processed < recount3 | RNA-seq data and associated metadata from a wide range of studies, enabling researchers to access < recount3 | and analyze gene expression data in a consistent manner. Recount3 aggregates data from multiple < recount3 | sources, including the < recount3 | Sequence Read Archive (SRA) < recount3 | and the < recount3 | Genotype-Tissue Expression (GTEx) project, < recount3 | and reprocesses it using a standardized pipeline. This allows for cross-study comparisons and < recount3 | meta-analyses, facilitating discoveries in genomics and transcriptomics. Processed recount3 data < recount3 | were integrated into the < recount3 | Snaptron system < recount3 | for indexing and querying data summaries. Recount3 is available < recount3 | at: http://rna.recount.bio. < recount3 |
< recount3 |< recount3 | These tracks display the recount3 intron data, including split read counts and splice junction < recount3 | motifs. For hg38, tracks are available for GTEx, TCGA, SRA, and CCLE data sources, while mm10 < recount3 | includes the SRA track only. < recount3 |
< recount3 | < recount3 |< recount3 | Intron items are colored based on splice junction motifs and read support. Darker colors indicate < recount3 | higher read coverage. Split read counts and splice motifs are shown on mouseover. < recount3 | By default, only introns with a minimum read count of 10,000 are shown. This threshold can be < recount3 | changed on the track configuration page. < recount3 |
< recount3 |< recount3 | The intron items are color-coded (darker colors indicate higher coverage): < recount3 |
< recount3 |< recount3 | Introns can be filtered by: < recount3 |
< recount3 |< recount3 | A distributed processing system for RNA-seq data called Monorail was developed. Using Monorail, < recount3 | recount3 processed and summarized 316,443 human and 416,803 mouse RNA-seq run accessions collected < recount3 | from the Sequence Read Archive (SRA), with the human runs including large-scale consortia such as < recount3 | GTEx v8 and The Cancer Genome Atlas (TCGA). < recount3 |
< recount3 |< recount3 | Junction files were converted to BED format. For grayscaling total read count was log10 < recount3 | transformed and multiplied by 10 to get a score between 0 and 225, which can be found < recount3 | in the BED score field. < recount3 |
< recount3 | < recount3 |< recount3 | The raw data can be explored interactively with the < recount3 | Table Browser or the < recount3 | Data Integrator. < recount3 | For automated analysis, the data may be queried from our < recount3 | REST API.
< recount3 |< recount3 | Please refer to our < recount3 | mailing list archives < recount3 | for questions or our < recount3 | Data Access FAQ < recount3 | for more information. < recount3 |
< recount3 |< recount3 | The original junction files for human can be found at: < recount3 |
< recount3 |< recount3 | The mouse junction file is available at: < recount3 |
< recount3 |< recount3 | Wilks C, Zheng SC, Chen FY, Charles R, Solomon B, Ling JP, Imada EL, Zhang D, Joseph L, Leek JT < recount3 | et al. < recount3 | < recount3 | recount3: summaries and queries for large-scale RNA-seq expression and splicing. < recount3 | Genome Biol. 2021 Nov 29;22(1):323. < recount3 | PMID: 34844637; PMC: PMC8628444 < recount3 |
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