Hi Brian,
I figured out the problem and a workaround.The problem is that even with your recommended settings reads that extended beyond the ends of both short and long reference sequences would only be mapped to the longer reference sequences.
The workaround is to avoid having longer and shorter reference sequences as mapping targets at the same time. I subdivided by reference sequences into multiple reference sequences that each contain sequences of the same size and then map against each of these individually. I can then merge the output from all of these mappings.
Thanks for your help this week and I hope my solution helps others who encounter the same issue!
dave
I figured out the problem and a workaround.The problem is that even with your recommended settings reads that extended beyond the ends of both short and long reference sequences would only be mapped to the longer reference sequences.
The workaround is to avoid having longer and shorter reference sequences as mapping targets at the same time. I subdivided by reference sequences into multiple reference sequences that each contain sequences of the same size and then map against each of these individually. I can then merge the output from all of these mappings.
Thanks for your help this week and I hope my solution helps others who encounter the same issue!
dave
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