8000 Global parameter for setting max intron length · Issue #169 · nf-core/rnasplice · GitHub
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Global parameter for setting max intron length #169

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KTMD-plant opened this issue Feb 28, 2025 · 0 comments
Open

Global parameter for setting max intron length #169

KTMD-plant opened this issue Feb 28, 2025 · 0 comments
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enhancement New feature or request

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Description of feature

When running nf-RNAseq it is recommended to set the max intron length to something suitable to your organism; for example in the model plant arabidopsis introns >6kb are very rare and running it with the default setting of 100MB will potentially give you some problematic artifacts. The parameter --allignIntronMax is passed to STAR in this pipeline. In rnasplice one currently needs to adjust config files which is tricky and if not done right can mess up a lot of behaviors. Novice users will run the pipeline in default mode and might not be aware of the effect this has on their results. Adding this feature would make it easier for casual users to adjust this parameter to something appropriate to their species.
@KTMD-plant KTMD-plant added the enhancement New feature or request label Feb 28, 2025
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