Hi-C and multi-mappers
Hi all,
I was wondering... what do you do with reads that map to multiple locations in a genome? For example, let's say that read1 maps uniquely next to a HindIII cleavage site and read2 equally maps to 3 locations of the genome, one of these locations is next to a HindIII cleavage site. Would you remove this paired-read? It might be informative.
I am asking this because the trend is to remove multi-mappers. However, I really think they are informative. What is your opinion about this topic?
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