Trimmomatic - MINLEN Default Value

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Hello,

I am trying to find the default value for MINLEN parameter. I used the tool with default parameters, specifying only to perform ILLUMINACLIP and adapter sequences on a set of paired-end reads. I did not set any Trimmomatic operation other than the default setting: SLIDINGWINDOW. Number of bases to average across is set to 4, and Average quality required is set to 20. If I were to include MINLEN, it is set to 20 by default. On the other hand, the examples from the lab’s website set MINLEN to 36, so I am not sure whether the default value is 36. I checked the Job Information under Details after the job was run. The command line and Tool Standard Output do not show the default value for MINLEN explicitly, as I did not set a MINLEN value. Then, I checked the log file but it also does not contain. I could only find examples in the manual, which also uses MINLEN:36, but I am not sure whether this is the default setting or just an example. I also tried trimming the same couple of reads with MINLEN:20 by just including the default Trimmomatic operation, but it generated files with different sizes, so I do not think the default is 20. Where can I find the default value used for MINLEN when not explicitly set?

Thank you for your consideration.

Edit: I used Trimmomatic on Galaxy.

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Hi,

as far as I know, if you’re not selecting a given operation like MINLEN, then it’s simply not performed at all, i.e. the default is not to drop any reads at all because of them being too short.

Now, in terms of what to set when you are using the operation, that depends a lot on your data. 36 from the documentation example is certainly not a bad recommendation because mapping reliability will decrease with less base information. On the other hand, if you are dealing with older sequencing data or poor quality one, enforcing 36 might just discard too much of the little data you have, in which case you might have to settle for a smaller value while being aware that mismappings have a higher chance to occur. Along the same lines, you might be able to increase the value to e.g. 50 with modern, state-of-the-art sequencing data.

Hope this helps,

Wolfgang

1 Like
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Dear Wolfgang,

Thank you for your swift reply!

Sincerely,

Beril