epic2 vs sicer2 1.0.3

[darked89]

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 Or maybe simply sicer2 implementation drifted from ca. 2019 and the combability of the outputs is no longer valid?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

epic2  \
--treatment 12_chip.bam \
--control 12_input.bam \
--genome  hg19 \
--autodetect-chroms \ 
--false-discovery-rate-cutoff 0.01 \
--output  12_0_epic2.out 

sicer2 run

sicer --verbose \
--cpu 12 \
--treatment_file 12_chip.bam \
--control_file 12_input.bam \
--species hg19 \
--false_discovery_rate 0.01 \
--significant_reads \
--output_directory 12_sicer2_out_dir