Repository containing raw data, scripts and circos configuration files to reproduce the genome plot.
| File | Description | Method summary |
|---|---|---|
Pseudo_Pac.fas |
Genome sequence | Assembled with RS_HGAP_Assembly.1 in SMRTanalysis 2.0.1, then manually cut and aligned |
Pseudo_Pac.gtf |
Genome annotation | Annotated in GenDB with default settings |
modifications.gff3 |
Modified bases | Methylation detection with RS_Modification_and_Motif_Analysis.1 in SMRTanalysis 2.0.1, using Pseudo_Pac.fas as the reference |
| File | Description | Method summary |
|---|---|---|
circos.conf |
Main CIRCOS configuration | Requires CIRCOS to run: http://circos.ca/software/download/circos |
gcSkew.pl |
Calculate GC content and skew | Modified from: https://github.com/Geo-omics/scripts/blob/master/AssemblyTools/gcSkew.pl |
| File | Description | Method summary |
|---|---|---|
gc_5000.gcSkew |
GC content and skew | Output of gcSkew.pl -f Pseudo_Pac.fas -w 5000 |
gc_5000.gc |
Raw GC content | Column with the GC content, taken from gc_5000.gcSkew |
gc_5000-62.46.gc |
Adjusted GC content | Absolute distances from the genome's mean GC content (62.46%) |
gc_5000.skew |
GC skew | Column with the GC skew, taken from gc_5000.gcSkew |
genes_heat_*.txt |
Methylation per gene | Relative methylation per gene, seperately for genes on plus and minus strand |
modifications_*.txt |
Genome-wide methylation | Absolute methylation per 2kb, 10kb and 50kb window, also strand-specific |
| Anything else | Mandatory CIRCOS files | Stuff like genome length, layout options, ... |
Plot of the complete Pseudomonas pseudoalcaligenes CECT5344 genome. The genome consists of 4,696,984 base pairs and 4,436 predicted coding sequences. The circles represent from the inside: 1, GC skew (red above and black below zero, 5kb window); 2, GC content (blue above and black below genome average of 62.46%, 5kb window); 3, strand-specific genome-wide methylation analyzed in 10kb windows; 4, strand-specific methylation per gene; 5, scale in million base pairs (Mb). Methylation color spectrum goes from blue (zero) over yellow (mean) to red (2*mean).