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PacificBiosciences / pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
BSD 3-Clause Clear License
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pigeon 1.1.0 and 1.2.0 output has issue to generate the reports similar to sqanti3. #629

Closed unique379r closed 9 months ago

unique379r commented 9 months ago

Hi I am trying to generate the report from "https://github.com/ConesaLab/SQANTI3/tree/master/utilities/report_pigeon" using the results of a pigeon but getting some errors:

sqanti3 issue: https://github.com/ConesaLab/SQANTI3/issues/236

Error in FUN(X[[i]], ...) : object 'within_cage_peak' not found
Calls: generatePDFreport ... <Anonymous> -> f -> scales_add_defaults -> lapply -> FUN
In addition: Warning messages:
1: Using alpha for a discrete variable is not advised.
2: Using alpha for a discrete variable is not advised.
3: Using alpha for a discrete variable is not advised.
4: Using alpha for a discrete variable is not advised.

Command used Rscript $report_pigeon/pigeon_report.R *_lite_classification.txt *_lite_junctions.txt $report_pigeon False both Note: I had no issue (still working) with pigeon_v1.0.0, but only with the new release (v1.1.0 and v1.2.0). I needed to update it as v1.0.0 was not producing the filt_summary.txt from the filter command.

unique379r commented 9 months ago

Never mind, I found the bug, pigeon new release > 1.0.0 has changed the name "cage" to "CAGE", which causes the issue to the script.