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
