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Feat: Built-in scoring for HMMRATAC #634
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A good suggestion. We will consider adding that. The way in JAVA HMMRATAC is to take the called regions and revisit the pileup signal tracks to compute these values. |
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Describe the solution you'd like
I'd like the option to calculate scores for peaks when running MACS3 HMMRATAC, similar to the original HMMRATAC implementation (the old command line option
--score <max || ave || med || fc || zscore || all>
). This would be useful for comparing peaks within a sample and enable downstream between-replicate reproducibility with methods like IDR.Describe alternatives you've considered
An alternative would be any type of informative peak scoring. Another suggestion would be a different version of the "fc" option where instead of reporting fold-change relative to the whole genome's average coverage, it reports fold change relative to the chromosome's average or a sliding-window local average.
Additional context
Currently, the gappedPeak files output by
macs3 hmmratac
contain all zeros for the score/signalValue/pValue/qValue columns, giving the impression that no peaks are higher confidence than the others.The text was updated successfully, but these errors were encountered: