This is my first time trying to use this package, which seems very useful for pulling out reads from a specific region ("-L"). However, for most of my applications I'm only interested in "properly paired" mates, i.e. those within some very small distance of each other, like 500bp or something. It is wildly inefficient to search the whole genome for mates that could be found locally. Is there a "--properly-paired-only" flag when using -L option, or have you considered such a feature? Thanks!
This is my first time trying to use this package, which seems very useful for pulling out reads from a specific region ("-L"). However, for most of my applications I'm only interested in "properly paired" mates, i.e. those within some very small distance of each other, like 500bp or something. It is wildly inefficient to search the whole genome for mates that could be found locally. Is there a "--properly-paired-only" flag when using -L option, or have you considered such a feature? Thanks!