besides the content that shown in .sam file(alignment of the best match, and number of suboptimal/all hits), seems it also contains some information of the suboptimal hits, is it possible to look at the details of these hits.
with the command "bwa samse -n INT", I can only get the position where they mapped and number of mismatch.
For paired-end data, whether "bwa sampe" consider the suboptimal hits? i.e., best-best match violate the distance constrain, but suboptimal-suboptimal or suboptimal-best may be in the rational distance.
with the command "bwa samse -n INT", I can only get the position where they mapped and number of mismatch.
For paired-end data, whether "bwa sampe" consider the suboptimal hits? i.e., best-best match violate the distance constrain, but suboptimal-suboptimal or suboptimal-best may be in the rational distance.
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