Thank you so much for your tools, and they really help!
However, I do have difficulty doing identifying differential peaks using SICER2. Could you provide any solutions?
For example, I wanted to identify differential H3K4me3 between HEK293 and K562. After preliminary analysis, I got four normalized bedgrph files, including H3K4me3 Hek293 bed, IgG Hek293 bed, H3K4me3 K562 bed, IgG K562 bed. However, I realized sicer_df in SICER2 only needs two groups of bed files as input ("sicer_df -t treatment1.bed treatment2.bed -c control1.bed control2.bed -s hg38"). However, I have four groups of bed files if I take IgG into account.
So, I am stuck in how to identify differential H3K4me peaks between cell lines.
Could you provide any solutions?
Thank you very much!
Thank you so much for your tools, and they really help! However, I do have difficulty doing identifying differential peaks using SICER2. Could you provide any solutions?
For example, I wanted to identify differential H3K4me3 between HEK293 and K562. After preliminary analysis, I got four normalized bedgrph files, including H3K4me3 Hek293 bed, IgG Hek293 bed, H3K4me3 K562 bed, IgG K562 bed. However, I realized sicer_df in SICER2 only needs two groups of bed files as input ("sicer_df -t treatment1.bed treatment2.bed -c control1.bed control2.bed -s hg38"). However, I have four groups of bed files if I take IgG into account. So, I am stuck in how to identify differential H3K4me peaks between cell lines. Could you provide any solutions? Thank you very much!