Hello,
I met one problem in the Tophat mapping. Does anyone know what the flag difference between 97 and 99 is?
The annotation of 99 is: read paired, read mapped in proper pair, mate reverse strand, first in pair
The annotation of 97 is: read paired, mate reverse strand, first in pair
Seems that the only difference is “read mapped in proper pair”. Is it due to the estimated insertion length? Can 97 be counted as a concordant pair?
Many thanks.
I met one problem in the Tophat mapping. Does anyone know what the flag difference between 97 and 99 is?
The annotation of 99 is: read paired, read mapped in proper pair, mate reverse strand, first in pair
The annotation of 97 is: read paired, mate reverse strand, first in pair
Seems that the only difference is “read mapped in proper pair”. Is it due to the estimated insertion length? Can 97 be counted as a concordant pair?
Many thanks.
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