Forum:Hard-Coded Bowtie2 Parameter '--B2-L' In Tophat
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8.2 years ago
hliang ▴ 100

I was testing different parameters of tophat2 recently. But I found that changing of some parameters has no effect, because they are fixed in the tophat source code (python).

Tophat 2 can pass parameters to Bowtie 2 by using Bowtie 2 option name prefixed with "--b2-". Parameter --b2-L is for setting the length of seed substrings, and it affects sensitivity and speed. It's hard-coded to 20. Another parameter --b2-gbar is hard-coded to 4.

If anyone is also running tophat with non-default parameter, I think this should be brought to their attention. I also wonder why the developers fix this values (although they work very well in most cases).

tophat2 bowtie2 Forum • 1.7k views
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Great post, but I changed it from a 'question' to a 'forum' post.

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