Output Files¶
Result files/folders are described as follows (main files/folders generated when using default options are followed by an asterisk):¶
| File or Folder | Description |
|---|---|
| result.json* | JSON file containing main information on detected CRISPR arrays and Cas genes on the program. |
| TSV* | Folder containing .tsv and .xls files. |
| Casfinder_summary_#sequenceID.tsv | Summary file generated by MacSyFinder. It contains information on Cas proteins. The option '-gscf' must be set to get this file. |
| Cas_REPORT.tsv* | File containing information on detected Cas systems and genes. This file is also available in Excel format. |
| CRISPR-Cas_clusters.tsv | File containing information on CRISPR arrays and Cas systems that are close to each other (e.g. separated by 20000 bp). The option '-ccc' is needed to get this file. |
| CRISPR-Cas_summary.tsv* | File containing summary information on both CRISPRs and Cas. This file is also available in Excel format. |
| CRISPR-Cas_systems_vicinity.tsv | File containing information on CRISPR arrays and their nearest Cas system, in function of a maximal distance defined with option 'vicinity'. The option '-ccvr' is needed to get this file. |
| crisprs_orientations_count.tsv | File showing a comparison between predictions made using precomputed results from CRISPRDirection versus AT% calculation in flanking regions. The option '-drpt' must be set to get this file. |
| Crisprs_REPORT.tsv* | File containing information on detected CRISPR arrays. This file is also available in Excel format. |
| GFF* | Folder containing GFF3 files. |
| annotation_#sequenceID.gff* | File generated by Prodigal or Prokka, containing CDS of the given sequence. |
| #sequenceID.gff* | File generated by CRISPRCasFinder, containing annotations of CRISPR arrays (repeats and spacers) as well as their flanking sequences. This file is specific and it cannot be viewed directly in Artemis or IGV contrary to the file generated by Prokka or Prodigal. |
| CasFinder | Folder containing files generated by MacSyFinder. |
| CRISPRFinderProperties | Folder containing files generated by the updated version of CRISPRFinder (CRISPR properties, FASTA files of DRs and spacers, and alignments). |
| LOGs | Folder containing log files (these files are generated if option "-log" was set). |
| logFile_DD_MM_YYYY_h_m_s.txt | File containing the output that CRISPRCasFinder produced during its run. |
| logSequences_DD_MM_YYYY_h_m_s.tsv | File containing some statistics related to the computation time for CRISPR and Cas searches and other features for each sequence. |
| Prodigal or Prokka | Folder containing files generated by either Prodigal (default option) or Prokka (if option "-prokka" was set). |
| rawFASTA | Folder containing FASTA sequences of all detected CRISPR arrays ("rawCRISPRs.fna") and Cas genes ("rawCas.fna"). FASTA files of analyzed sequences are also contained in this folder. |
| Visualization | Folder containing an HTML page and a CSS file allowing to visualize CRISPRs and Cas with the same design as CRISPRdb (these files are generated if options "-html" and "-copyCSS" were set). |
When using CRSIPRCasFinder.pl, all secondary folders will be deleted by default unless the option "-keep" is set.
"#sequenceID" represents the ID of analyzed sequence(s).
"DD_MM_YYYY_h_m_s" represents the current date (day, month, and year) and time (hours, minutes, and seconds).