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qqwang-berkeley / JUM

A tool for annotation-free differential analysis of tissue-specific pre-mRNA alternative splicing patterns
MIT License
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PSI values per condition #35

Closed lhdo closed 3 years ago

lhdo commented 3 years ago

How would I go about calculating the PSI values per condition (i.e. PSI for control and PSI for treatment) for each event type? Currently, I only see the delta PSI values reported from both the simplified and detailed output files. Any help would be greatly appreciated! Thanks!

qqwang-berkeley commented 3 years ago

Hi, sorry for the late reply. If you want to calculate the PSI value per condition, one work around is to check the following columns in the detailed output files: raw_count.ctrl1 raw_count.ctrl2 raw_count.ctrl3 raw_count.treat1 raw_count.treat2 raw_count.treat3 percentage_usage.ctrl1 percentage_usage.ctrl2 percentage_usage.ctrl3 percentage_usage.treat1 percentage_usage.treat2

These columns record the raw counts to each sub_AS_junction in every AS_structure (for the definition of AS structure, please refer to the JUM manuscript), and if you refer to the manual about the definition of PSI for each event type (detailed in the "output" part in the manual), you should be able to calculate the PSI values per condition. These values are put there to give users an idea about the raw outcome as well.