SEQanswers - View Single Post - Tophat2 very slow when running over Bowtie2

jdenvir · 02-18-2013, 05:28 AM

I ended up running Tophat2 over Bowtie 1; the latest version of each resolved the problems I was having with crashing. It would be nice to understand why Bowtie2 is prohibitively slow, though.

02-18-2013, 05:28 AM	#3
jdenvir Junior Member Location: Huntington, WV USA Join Date: Dec 2011 Posts: 6	I ended up running Tophat2 over Bowtie 1; the latest version of each resolved the problems I was having with crashing. It would be nice to understand why Bowtie2 is prohibitively slow, though.