| Title: | Strand-seq data for demonstration purposes |
|---|---|
| Description: | Strand-seq data to demonstrate functionalities of breakpointR package. |
| Authors: | David Porubsky, Aaron Taudt, Ashley Sanders |
| Maintainer: | David Porubsky <[email protected]> |
| License: | file LICENSE |
| Version: | 1.31.0 |
| Built: | 2026-10-10 10:39:07 UTC |
| Source: | https://github.com/bioc/breakpointRdata |
A set of BAM-files for demonstration purposes of the functions in package breakpointR.
A BAM files with aligned reads with one read per line.
BAM files contain single-end reads aligned to GRCh38 reference genome.
Read sequences and quality values have been removed in order to reduce the file size.
A lyphoblastoid cell line of Puerto Rican origin (HG00731). Raw reads were aligned to the GRCh38/hg38 reference assembly. The file has been downsampled to 20% of the coverage to reduce the file size.
https://www.biorxiv.org/content/early/2017/09/23/193144
Localized breakpoints in example BAM-files, generated by the breakpointR package.
Files containing BreakPoint object.
A BreakPoint object is a list containing given elements: ID, fragments, deltas, breaks, confint, counts, lib.metrics and params.
ID - unique identifier for a given library.
fragments - A GRanges-class object that stores analyzed sequencing reads.
deltas - A GRanges-class object that stores binned minus reads differences.
breaks - A GRanges-class object that stores localized breaks.
confint - A GRanges-class object that stores confidence intervals around localized breaks.
counts - A GRanges-class object that stores directional read counts in between localized breaks.
lib.metrics - A named vector with some useful library metrics.
params - A named vector with user defined parameters used to run breakpointR package.
A lyphoblastoid cell line of Puerto Rican origin (HG00731). Raw reads were aligned to the GRCh38/hg38 reference assembly.
https://www.biorxiv.org/content/early/2017/09/23/193144