CATS_rf_compareCATS-rf also supports direct comparison of multiple analysed assemblies. The CATS_rf_compare script generates summary tables and visualizations that compare the most significant CATS-rf results of each assembly. As such, CATS-rf should be run on each individual assembly and the resulting CATS-rf output directories should then act as input to CATS_rf_compare.
CATS_rf_compare dependenciesCATS_rf_compare requires the following dependencies:
| Dependency | Tested Version | Homepage | Conda Installation | R installation |
|---|---|---|---|---|
| R | 4.3.0.-4.4.3 | https://www.r-project.org | conda install conda-forge::r-base |
/ |
| pandoc | 2.19.2 | https://pandoc.org/ | conda install conda-forge::pandoc |
/ |
| rmarkdown (R) | 2.29 | https://cran.r-project.org/package=rmarkdown | conda install conda-forge::r-rmarkdown |
install.packages("rnarkdown) |
| data.table (R) | 1.16.4 | https://cran.r-project.org/package=data.table | conda install conda-forge::r-data.table |
install.packages("data.table") |
| ggplot2 (R) | 3.5.1 | https://cran.r-project.org/web/packages/ggplot2 | conda install conda-forge::r-ggplot2 |
install.packages("ggplot2") |
| ggdist (R) | 3.3.2 | https://cran.r-project.org/web/packages/ggdist | conda install conda-forge::r-ggdist |
install.packages("ggdist") |
R (Rscript) executable must be included in PATH. Tools denoted with (R) correspond to R packages and can be installed via conda or directly in R with the supplied commands.
CATS_rf_compare example usageCATS_rf_compare requires one or more CATS-rf output directories as input.
While CATS_rf_compare is primarily designed to compare multiple transcriptome assemblies, it can also be used with a single assembly to visualize its CATS-rf results.
Example CATS_rf_compare usage:
CATS_rf_compare [OPTIONS] CATS_RF_DIR ...
CATS_rf_compare optionsCATS_rf_compare offers a comprehensive list of options which allow users to control the graphical and general comparison parameters.
-x: Figure extension, default: png
-d: Figure DPI, default: 600
Extension (device) and DPI of each plotted figure are controlled with x and d, respectively.
-r: Raincloud plot colors (quoted hexadecimal codes or R color names, specified with x,y,z…), default: adjusted Set1 palette from RColorBrewer package
Raincloud plot densities are normalized for each transcriptome assembly. Boxplots within raincloud plots mark the distribution median, Q1, and Q3, with whiskers extending from Q1 - 1.5 * IQR to Q3 + 1.5 * IQR of the distribution.
All color sets (r, l, H, and b) should be supplied as R color names or hexadecimal codes separated with commas and enclosed in quotes (e.g. “#FDAF4A,#DC151D”). R color cheatsheet is available here.
-l: Lineplot colors (quoted hexadecimal codes or R color names, specified with x,y,z…), default: adjusted Set1 palette from RColorBrewer package
-H: Histogram colors (quoted hexadecimal codes or R color names, specified with x,y,z…), default: adjusted Set1 palette from RColorBrewer package
-b: Barplot colors (quoted hexadecimal codes or R color names, specified with x,y,z…), default: adjusted YlOrRd palette from RColorBrewer package
-q: Maximum right-tail distribution quantile for histograms, default: 0.98”
Histograms show relative density per transcriptome assembly and omit right-tail extreme values for visualization purposes. The x-axis in all histograms is square-root scaled.
-t: Number of CPU threads, default: 10
Several steps of CATS_rf_compare are parallelized. This mainly includes operations performed by the data.table package. Recommended number of threads: 8-12.
-D: Comparison output directory name, default: CATS_rf_comparison
-O: Overwrite the comparison output directory, default: off
-h: Show usage information
CATS_rf_compare output explanationThe analysis is summarized in the CATS_rf_comparison.html HTML file.
An example of the HTML output is provided here.
Note on transcriptome assembly order and names: Assemblies will appear in the order they were provided on the command line when running the tool. For visualization purposes, assembly names are limited to a maximum of 20 characters; names exceeding this limit will be truncated. If multiple assemblies share the same name, a numeric suffix (e.g., .1, .2, etc.) will be appended to distinguish these assemblies.
CATS_rf_compare aggregates individual summary tables into comprehensive joint tables encompassing all analyzed transcriptome assemblies:
CATS_rf_general_statistics.tsv contains aggregated CATS-rf general statistics table.
CATS_rf_assembly_scores.tsv contains aggregated CATS-rf score component statistics and overall assembly score table.
CATS_rf_coverage_accuracy_statistics.tsv contains aggregated CATS-rf coverage and accuracy analysis table.
CATS_rf_local_fidelity_integrity_statistics.tsv contains aggregated CATS-rf paired-end read analysis table.
CATS_rf_compare produces several figures, providing a detailed visualization of CATS-rf quality metrics.
transcript_score visualizes the distribution of transcript scores.
base_coverage and base_accuracy visualize the distribution of per-base coverage/accuracy.
proportion_of_covered_bases visualizes the distribution of the proportion of covered bases per transcript.
mean_transcript_coverage visualizes the distribution of mean transcript coverage.
positional_relative_coverage_median and positional_accuracy_median visualize the positional relative coverage/accuracy distribution.
maximum_uncovered_region_length visualizes the distribution of maximum uncovered region length per transcript.
mean_transcript_end_coverage visualizes the distribution of mean transcript end coverage.
proportion_of_bases_in_lcrs and proportion_of_bases_in_lars visualize the distribution of the proportion of bases in LCRs/LARs per transcript.
lcr_length and lar_length visualize the distribution of LCR/LAR length.
coverage_score_component visualizes the distribution of coverage score component per transcript.
proportion_of_accurate_bases visualizes the distribution of the proportion of accurate bases per transcript.
accuracy_score_component visualizes the distribution of accuracy score component per transcript.
proportion_of_improperly_paired_reads visualizes the per-transcript distribution of the proportion of improperly paired reads within a transcript.
local_fidelity_score_component visualizes the distribution of local fidelity score component per transcript.
prop_reads_with_pair_mapped_to_another_tr visualizes the per-transcript distribution of the proportion of reads with pair mapped to another transcript.
integrity_score_component visualizes the distribution of integrity score component per transcript.