PLOTSR on Biowulf
Plotsr generates high-quality visualisation of synteny and structural rearrangements between multiple genomes. For this, it uses the genomic structural annotations between multiple chromosome-level assemblies.
References:
- Manish Goel, Korbinian Schneeberger plotsr: visualizing structural similarities and rearrangements between multiple genomes Bioinformatics, Volume 38, Issue 23, 1 December 2022, Page 5328
Documentation
Important Notes
- Module Name: remora (see the modules page for more information)
- Multithreaded
- Environment variables set
- REMORA_HOME
- Example files in /usr/local/apps/plotsr/1.1.0/example
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program.
Sample session (user input in bold):
[user@biowulf]$ sinteractive [user@cn4338 ~]$ module load plotsr [+] Loading plotsr 1.1.0 on cn4326 [+] Loading singularity 3.10.5 on cn4326
Example
Most jobs should be run as batch jobs.
Running help command:
[user@cn4338] cp -a /usr/local/apps/plotsr/1.1.0/example .
[user@cn4338 example]$ plotsr -h
usage: Plotting structural rearrangements between genomes [-h] [--sr SR] [--bp BP]
--genomes GENOMES
[--markers MARKERS]
[--tracks TRACKS]
[--chrord CHRORD]
[--chrname CHRNAME] [-o O]
[--itx] [--chr CHR] [--reg REG]
[--rtr] [--nosyn] [--noinv]
[--notr] [--nodup] [-s S]
[--cfg CFG] [-R] [-f F] [-H H]
[-W W] [-S S] [-d D]
[-b {agg,cairo,pdf,pgf,ps,svg,template}]
[-v] [--lf LOGFIN]
[--log {DEBUG,INFO,WARN}]
[--version]
Input/Output files:
--sr SR Structural annotation mappings (syri.out) identified by SyRI
(default: None)
--bp BP Structural annotation mappings in BEDPE format (default: None)
--genomes GENOMES File containing path to genomes (default: None)
--markers MARKERS File containing path to markers (bed format) (default: None)
--tracks TRACKS File listing paths and details for all tracks to be plotted
(default: None)
--chrord CHRORD File containing reference (first genome) chromosome IDs in the
order in which they are to be plotted. File requires one
chromosome ID per line. Not compatible with --chr (default: None)
--chrname CHRNAME File containing reference (first genome) chromosome names to be
used in the plot. File needs to be a TSV with the chromosome ID
in first column and chromosome name in the second. (default:
None)
-o O Output file name. Acceptable format: pdf, png, svg (default:
plotsr.pdf)
Data filtering:
--itx Use inter-chromosomal plotting mode (experimental) (default:
False)
--chr CHR Select specific chromosome on reference (first genome) and plots
them in the given order. Not compatible with --chrord. Can be
used multiple time to select more than one chromosomes. (default:
None)
--reg REG Plots a specific region. Use as: GenomeID:ChromosomeID:Start-End.
Not compatible with --chr and -R. (default: None)
--rtr When using --reg, plot all SRs that are within the boundaries of
the homologous regions. For highly zoomed regions, this could
result in visually disconnected alignments. (default: False)
--nosyn Do not plot syntenic regions (default: False)
--noinv Do not plot inversions (default: False)
--notr Do not plot translocations regions (default: False)
--nodup Do not plot duplications regions (default: False)
-s S minimum size of a SR to be plotted (default: 10000)
Plot adjustment:
--cfg CFG Path to config file containing parameters to adjust plot.
(default: None)
-R Join adjacent syntenic blocks if they are not interrupted by SRs.
Using this would decrease gaps in the visualisation. (default:
False)
-f F font size (default: 6)
-H H height of the plot (default: None)
-W W width of the plot (default: None)
-S S Space for homologous chromosome (0.1-0.75). Adjust this to make
more space for annotation markers/texts and tracks. (default:
0.7)
-d D DPI for the final image (default: 300)
-b {agg,cairo,pdf,pgf,ps,svg,template}
Matplotlib backend to use (default: agg)
-v Plot vertical chromosome (default: False)
optional arguments:
-h, --help show this help message and exit
--lf LOGFIN Name of log file (default: plotsr.log)
--log {DEBUG,INFO,WARN}
Log-level (default: WARN)
--version show program's version number and exit
Example Visualization
## Unzip gene annotation and SNPs file. These would be plotted as tracks. [user@cn4338] cp -a /usr/local/apps/plotsr/1.1.0/example . [user@cn4338] cd example/ [user@cn4338 example]$gzip -d TAIR10_GFF3_genes.gff.gz [user@cn4338 example]$ gzip -d 1001genomes.snps.sorted.bed.gz # Plot using plotsr [user@cn4338 example]$ plotsr \ --sr col_lersyri.filtered.out \ --sr ler_cvisyri.filtered.out \ --sr cvi_erisyri.filtered.out \ --genomes genomes.txt \ -o output_plot.png 2024-01-17 13:31:14,247 - Plotsr - INFO - Starting 2024-01-17 13:31:17,163 - Plotsr - INFO - Plot output_plot.png generated. 2024-01-17 13:31:17,163 - Plotsr - INFO - Finished
| For more examples, please visit the Plotsr Example Github Page |