Trimmomatic: LEADING and TRAILING

Question

[Bioinfonext]

I am not able to understand what is the meaning of LEADING:5 and TRAILING:5?

how 5 indicate here about the quality of the base score. I understand phred score which generally we give between 10 to 40. phred score 10 means 1-time base may be wrong in the read if the read is sequenced 10 times.

But not able to understand LEADING and TRAILING value?

Answer 1

[Matteo Schiavinato]

Trimmomatic will trim bases at the beginning (i.e. "LEADING") or at the end ("TRAILING") of your read if their quality score falls below the value specified after the colon (":").

Have a look at their manual: http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf

[Bioinfonext]

Thanks, That I understood what they do? but how value 5 defines the quality of the base?

[Bioinfonext]

Does here LEADING and TRAILING value is also phred score? If Yes, then why people give it 3 or 5?

[WouterDeCoster]

From the manual

quality: Specifies the minimum quality required to keep a base.

the basecall phred score, indeed

[Bioinfonext]

Thanks, Could you please suggest what should be the value for LEADING and TRAILING, will it be ok if I give 10 or 20.

[Matteo Schiavinato]

Also, there is no such thing as "what it should be". It depends on the data, on the quality of your sequencing, on the risks you're willing to take. Thresholds are just something we put, but they don't define perfection. What is important, is that you understand the rationale behind it in order to make an educated choice (here and everywhere in science, sorry for going phylosophical).

[finswimmer]

Unless the overall quality of your bases isn't really bad, don't trim your data. You will throw away information that might be useful.

These "quality-trimming-thing" is from a time where the sequencing quality was quite poor and you have a significant drop off of the quality towards the end of the reads. This doesn't happen that dramatically nowadays.

fin swimmer

[WouterDeCoster]

Of course it also depends on the application

[lieven.sterck]

unless you have a very specific objective I would go for at least 20 (perhaps even 25-26 nowadays)

[MSF]

Im sorry, but still I did not understand the value? So when writing in your code LEADING:5, it will look for phred score5 per se? I mean why would anyone keep a base with a such low quality value? or is there something I missed?