Comments (3)
It is likely that you don't have any clusters that the alignment script considers core i.e. >95% of isolates and dosage/copy number <1.25. You can check that this is the case in the tabular output in the log or summary file. If this is the case and you want to modify the default thresholds to use a more relaxed core definition then you can run the script(s) manually.
create_pangenome_alignment.pl -i /path/to/PIRATE.gene_families.tab -f /path/to/feature_sequences/ -o /path/to/output_fasta.fasta -g /path/to/output_gff.gff -t percentage_threshold (integer) -d dosage_threshold(floating_point)
If dosage/copy number is an issue you may have a problematic dataset. If this is the case let me know and I can suggest some advanced settings that should improve cluster resolution.
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Is there somewhere where the options for core threshold and dosage threshold are documented?
I'm running PIRATE v.1.0.3 and the "-t" option seems to set threads, not core threshold, and I can't find the "-d" option in any of the help menus.
Thanks!
Conrad
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Hi Conrad,
You will need to run the script create_pangenome_alignment.pl (in /PIRATE/scripts/ directory) separately as detailed above. There is currently no options for changing these defaults from the main PIRATE script. I will consider adding them in a future update.
All the best,
Sion
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Related Issues (20)
- Confused with terminology/output HOT 1
- extract_feature_sequences.pl failed HOT 2
- error observed during "aligning all feature sequences" HOT 2
- Missing genome in output HOT 12
- Output gene sequences to run gene alignment separately HOT 4
- PIRATE_plots.pdf created by plot_summary.R HOT 1
- Error after MCL clustering step HOT 5
- How do you tell which gene families are single-copy or multi-copy? HOT 2
- Feature request: Option to include original IDs and annotations in fasta headers for align_features_sequences script HOT 2
- Average_dose =1 is appropriate to determine whether a gene family is a single copy? HOT 1
- - ERROR: link_clusters.pl failed. HOT 1
- Undefined subroutine &main::translate called HOT 2
- Error when running PIRATE MCL process
- For some single loci, a gene family but for others not. HOT 1
- problem in installation HOT 9
- Bump version in new release HOT 4
- Missing output files and coregenom files HOT 3
- Running on large dataset HOT 2
- stuck at threshold 60 during MCL clustering HOT 3
- PIRATE.pangenome_summary.txt HOT 6
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