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9.8 years ago
zioutisch
•
0
I tried to run Tophat with different bowtie2 options. I actually used the preset bowtie2 options (i.e. --b2-sensitive). Looking for differences between different runs, i checked the align_summary.txt files for each run and what i got was exactly the same alignment rate. So, i assumed that Tophat aligned the reads with its default options in all cases , ignoring mine. Could anyone help me understand why this happens or experiences the same problem?
Have a look in the run log from each test. There, you'll find the exact bowtie2 commands that tophat is using and can directly check if it's ignoring your settings or not. I should note that a number of settings do seem to be hard-coded.
Thank you for your reply. I checked the run log files and it seems that tophat uses my specified options to call bowtie2, so I can't figure out what is happening. Is there any case of tophat's bug?