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looks like the sicer2 did implement the fix to handle beyond the ends of chromosomes reads. But somehow the results between these two programs differ. epyc2: 13_642 peaks, sicer2 35_257 peaks. The commands / parameters I have used are below.
Changing / adding for sicer2 --window_size 100 and --fragment_size 100 brought the number of peaks to 27_585, but the differences are still huge. When these BED results were checked in IGV, epic2/sicer2 peaks seldom overlapped.
Do I somehow use incompatible program parameters causing such differences? Or maybe simply sicer2 implementation drifted from ca. 2019 and the combability of the outputs is no longer valid?
Hello,
looks like the sicer2 did implement the fix to handle beyond the ends of chromosomes reads. But somehow the results between these two programs differ. epyc2: 13_642 peaks, sicer2 35_257 peaks. The commands / parameters I have used are below.
Changing / adding for sicer2
--window_size 100
and--fragment_size 100
brought the number of peaks to 27_585, but the differences are still huge. When these BED results were checked in IGV, epic2/sicer2 peaks seldom overlapped.Do I somehow use incompatible program parameters causing such differences? Or maybe simply sicer2 implementation drifted from ca. 2019 and the combability of the outputs is no longer valid?
Many thanks for your help
Darek Kedra
epic2 run
sicer2 run
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