default rule filter also filtered out mono-exonic transcripts

[MengjunWu]

Is there an existing issue for this?

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• I have loaded the SQANTI3.env conda environment

Problem description

Hi,

I am using the default rule filter in Sqanti3 to filtered out artefacts, while the parameters file stated "FilterMonoexonic False". I noticed all the mono-exonic transcripts that are not in the full splice match category are also labeled as artifacts -- these filtered out mono-exonic transcripts are not listed in the "filtering_reason.txt" file but excluded in the final "inclusion-list.txt" file. Is this filtering actually automatically turned on when running Sqanti3 filtering?

Many thanks!
Mengjun

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