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Nanoblot: an R-package for visualization of RNA isoforms from long-read RNA-sequencing data.
| Content Provider | eScholarship Repository: University of California |
|---|---|
| Author | DeMario, Samuel Xu, Kevin He, Kevin Chanfreau, Guillaume |
| Abstract | RT-PCR and northern blots have long been used to study RNA isoforms usage for single genes. Recent advancements in long-read sequencing have yielded unprecedented information about the usage and abundance of these RNA isoforms. However, visualization of long-read sequencing data remains challenging due to the high information density. To alleviate these issues, we have developed NanoBlot, an open-source R-package that generates northern blot and RT-PCR-like images from long-read sequencing data. NanoBlot requires aligned, positionally sorted and indexed BAM files. Plotting is based around ggplot2 and is easily customizable. Advantages of NanoBlot include a robust system for designing probes to visualize isoforms including excluding reads based on the presence or absence of a specified region, an elegant solution to representing isoforms with continuous variations in length, and the ability to overlay multiple genes in the same plot using different colors. We present examples of nanoblots compared to actual northern blot data. In addition to traditional gel-like images, the NanoBlot package can also output other visualizations such as violin plots and 3-RACE-like plots focused on 3-end isoforms visualization. The use of the NanoBlot package should provide a simple answer to some of the challenges of visualizing long-read RNA-sequencing data. |
| File Format | |
| DOI | 10.1261/rna.079505.122 |
| Alternate Webpage(s) | https://escholarship.org/uc/item/259674z0 |
| Journal | RNA |
| Issue Number | 8 |
| Volume Number | 29 |
| Language | English |
| Publisher Date | 2023-08-01 |
| Access Restriction | Open |
| Rights License | https://creativecommons.org/licenses/by-nc/4.0/ |
| Subject Keyword | Alternative Polyadenylation Alternative Splicing Data Visualization Isoform Visualization Long-Read Sequencing Nanopore Sequencing RNA RNA Isoforms High-Throughput Nucleotide Sequencing Sequence Analysis Protein Isoforms Gene Expression Profiling Transcriptome |
| Content Type | Text |
| Resource Type | Article |
