Question: Bowtie2 settings in Tophat
gravatar for zioutisch
5.7 years ago by
zioutisch0 wrote:

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?

rna-seq alignment • 1.8k views
ADD COMMENTlink written 5.7 years ago by zioutisch0

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.

ADD REPLYlink written 5.7 years ago by Devon Ryan94k

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? 

ADD REPLYlink written 5.7 years ago by zioutisch0
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