Question: Presets And Dependent Parameters For Bowtie2/Tophat2
1
6.1 years ago by
blair20
Cambridge, MA
blair20 wrote:

[Edited for clarity]. If you enter a preset option and its dependent parameters in Bowtie or TopHat, which one will override and be implemented? For example, there are the four preset options (fast, very fast, sensitive, very sensitive). So if I run bowtie2 --very sensitive, it will set the following parameters ( -D 20 -R 3 -N 0 -L 20 -i S,1,0.50. ). But what if I enter bowtie2 --very sensitive and -D 10. Which effort option do I get? D= 10 or D = 20?

bowtie2 tophat2 • 2.0k views
modified 5.3 years ago by Biostar ♦♦ 20 • written 6.1 years ago by blair20

Could you be more elaborate ?

I keep reading the question over and over again, and I have no idea what is actually being asked. Preset options are usually over-ridden by parameters on the command-line (i.e. default values are set and used, unless the user specifies differently). Can you elaborate with an example?

Hey all, sorry for the confusing question. Hope I can clarify. There are the four preset options (fast, very fast, sensitive, very sensitive). So if I run bowtie2 --very sensitive, it will set the following parameters ( -D 20 -R 3 -N 0 -L 20 -i S,1,0.50. ). But what if I enter bowtie2 --very sensitive and -D 10. Which effort option do I get? D= 10 or D = 20?

Thanks for the example. I would recommend the following: 1.) edit your question and insert your example (for clarity, good posterity, and to increase the likelihood that someone will answer your question), and 2.) if someone does not already know the answer, you could perform a test - if you have a simple situation in which you can determine the outputs of the different options, test to see what the effect of changing D is. (It could be something as simple as taking a set of reads and putting "time" in front of your commands.) Or 3) you could write the author directly. Either way, make sure to report your results back here! :)

Thanks seidel. Implemented suggestion 1. Will probably go for option 2 when I get some spare time. Will surely report back when I sort it out.

I think you can try using D=10 and then check the bowtie2 log files to know what parameters id bowtie2 end up using. Bowtie2 will print all the parameters it used for the alignment. Though I am not sure if you can get exact information for parameters like -D,-R etc.

I was thinking on check this myself too. Finally I decided not to use the presets options anymore when tuning parameters, so I just use in those cases the whole bunch of -D 20 -R 3 -N 0 -L 20 -i S,1,0.50.

However, if you want to check, @ashutoshmits says correctly that you can check that on the log files, specially logs/run.log, where everycommand run by TopHat is printed along with all the parameters used. However, I guess you will find that TopHat is only pasting your parameters, so both the preset and the custom parameter will go there. If you plan to check this by checking results, be aware that results sometimes are fiddly to interpret. For example, I changed the -N 1, and I found that I have a lower number of results, mappings, that with -N 0.

Have do you finally find an answer to this?

ADD REPLYlink modified 5.6 years ago • written 5.6 years ago by cpcantalapiedra140