Description:
I'm preparing to use hicDifferentialTAD for differential TAD analysis between two Hi-C datasets (treatment and control). I have matrices in .h5 format obtained after normalization (hicNormalize -m "$file" --normalize smallest). However, I need clarification on whether these .h5 files should be corrected (hicCorrectMatrix) before normalization for use in hicDifferentialTAD.
Context:
From my understanding, Hi-C data typically undergoes correction (e.g., ICE correction) followed by normalization to minimize technical biases. Should the matrices used in hicDifferentialTAD be corrected and then normalized, or is it acceptable to normalize .h5 files directly without prior correction?
Expected Clarification:
Could you please confirm whether hicDifferentialTAD expects .h5 matrices that have undergone both correction and normalization steps, or if normalization alone (without prior correction) is sufficient for accurate differential TAD analysis?
Thank you for your assistance in providing clarity on this matter.
Description: I'm preparing to use hicDifferentialTAD for differential TAD analysis between two Hi-C datasets (treatment and control). I have matrices in .h5 format obtained after normalization (hicNormalize -m "$file" --normalize smallest). However, I need clarification on whether these .h5 files should be corrected (hicCorrectMatrix) before normalization for use in hicDifferentialTAD.
Context: From my understanding, Hi-C data typically undergoes correction (e.g., ICE correction) followed by normalization to minimize technical biases. Should the matrices used in hicDifferentialTAD be corrected and then normalized, or is it acceptable to normalize .h5 files directly without prior correction?
Expected Clarification: Could you please confirm whether hicDifferentialTAD expects .h5 matrices that have undergone both correction and normalization steps, or if normalization alone (without prior correction) is sufficient for accurate differential TAD analysis?
Thank you for your assistance in providing clarity on this matter.