Thank you a bunch Heng! Best, Hongdong
On Tue, Aug 4, 2015 at 11:18 AM, Heng Li <[email protected]> wrote: > > On Aug 3, 2015, at 11:15 PM, Hongdong Li <[email protected]> > wrote: > > > Hello Heng, > > > > Thanks a lot for your great samtools! I am recently using it to > extract reads overlapping with intron regions. I first used samtools view > -L somebedfile. Regarding the overlapping with regions defined in bedfile, > I have two questions here: first, how many bases are required to claim a > read overlaps a region in a bedfile, at least one base or any threshold? > > One base. > > > Second, for the bedfile, does it need any other field (columns) in > addition to the mandatory 3 columns containing ref, start and end position. > Your help would be highly appreciated! > > Columns beyond the first three are ignored. > > Heng > > > > > Best, > > Hongdong > > > >
------------------------------------------------------------------------------
_______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
