gmap參數

--min-intronlength 最小intron的長度. 挪威雲杉最短intron是34

--max-intronlength-middle 基因中間最長intron的長度.   挪威雲杉最長intron是68,269 Note: for backward compatibility, the -K or --intronlength flag will set both --max-intronlength-middle and --max-intronlength-ends.

-n Maximum number of paths to show. Maximum number of paths to show (default 5).  If set to 1, GMAP will not report chimeric alignments, since those imply two paths.  If you want a single alignment plus chimeric alignments, then set this to be 0.      -n取1的時候能夠去除多定位

-t number of threads

-f format of output