Hi all,
I was trying to find the inward oriented pairs (innies) and outward oriented pairs (outties) using Bamcheck and Samtools. Both gave me different results on running. May I know which one to pick from both? Any suggestions or comments are welcome!
My guess would be that these are handling dovetailed and or bookended reads differently. Since the files are small, just subset them until you find a single alignment that causes the numbers to differ and then have a look at that.
Thanks Devon Ryan. I will try to look at that. May I know what it means by dovetailed and bookended reads?
That nomenclature is borrowed from bowtie2, though I probably meant "contain" rather than "bookend".