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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:
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.
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: