Detailed Tutorial - nselem/corason GitHub Wiki

CORASON Tutorial

$ corason.pl -rast_ids rastIds -q query -s special_org [-hv] [-e_value query_evalue] [-c number_of_genes_on_cluster] [-b bit_score] [-e_cluster cluster_e_value] [-e_core core_e_value] [-l genome_selected] [-rescale number]

Box Plots

Bubble Chart

Bullet Charts

Calendar View

**--rast_ids ** Required (No Default) RAST ids tab-separated table. From Rast: Job id\tGenome id\tOrganism name.

--queryfile,-q Required (No default) Your aminoacid sequence on fasta file.

--special_org,-s Required (No default) Job Id (from RAST) for the cluster where your query belongs.

--e_value Default: 1E-15 (float) E value. Minimal for a gene to be considered a hit.

--bitscore,-b Default: 0 (Positive integer) After one run look into file .BLAST.pre to be more restrictive on hits.

--cluster_radio -c Default: 10 (Positive integer) Number of genes in the neighborhood to analize.

--e_cluster Default: 1E-3 (float) e-value for sequences from reference cluster, values above it will be colored.

--e_core Default: 1E-3 (float) e-value for Best Bidirectional Hits used to cunstruct genomic core from clusters.

--list Default: GENOME/*.faa (string separated by "," or ":". Example 1,2,4:6 produce a search on genomes 1,2,4,5,6) Leaving this option empty will conduce to search on all genomes in GENOME directory.

--rescale,r Default: 85000 (integer) Increasing this number will show a bigger cluster region with smaller genes.

--verbose,v If you would like to read more output from scripts. Most of the time only useful if you would like script debugging.

Remarks: For float values (as e_value, e_core etc) 0.001 will work, but .001 won't do it.