Hey everyone, 
I'm in a bit of a pickle trying to figure out the way the output in bowtie2 is different from the bowtie'1' output. My problem is the following:
Setting -I min and -X max for expected insert size interval are parameters of both aligners. However, bowtie2 still outputs pairs pairing with isizes smaller than -I or bigger than -X. Changing this interval also affects the insert size distribution, so it's not like these parameters are ignored. Does anyone know why, or have any additional insight that could help me trust bowtie2 more?
-Alex
I'm in a bit of a pickle trying to figure out the way the output in bowtie2 is different from the bowtie'1' output. My problem is the following:
Setting -I min and -X max for expected insert size interval are parameters of both aligners. However, bowtie2 still outputs pairs pairing with isizes smaller than -I or bigger than -X. Changing this interval also affects the insert size distribution, so it's not like these parameters are ignored. Does anyone know why, or have any additional insight that could help me trust bowtie2 more?
-Alex
