Comments (2)
liz-is
commented on June 9, 2024
Hi Jorge,
Bias due to CNVs is typically accounted for during the matrix balancing step of producing Hi-C matrices. CHESS takes balanced matrices as input, as stated in the documentation. Depending on the nature of the CNV, there may be changes in the Hi-C matrix that aren't removed by matrix balancing and are then picked up by CHESS, but over/under-representation of a region that varies in copy number should be accounted for already.
from chess.
jazberna1
commented on June 9, 2024
Hello Liz,
Thanks so much for the clarification!
Regards
Jorge
from chess.
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from chess.