Question: Trimmomatic: LEADING and TRAILING
0
gravatar for Bioinfonext
4 weeks ago by
Bioinfonext120
Korea
Bioinfonext120 wrote:

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?

next-gen • 132 views
ADD COMMENTlink modified 4 weeks ago by Macspider2.7k • written 4 weeks ago by Bioinfonext120
2
gravatar for Macspider
4 weeks ago by
Macspider2.7k
Vienna - BOKU
Macspider2.7k wrote:

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

ADD COMMENTlink written 4 weeks ago by Macspider2.7k

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

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by Bioinfonext120

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

ADD REPLYlink written 4 weeks ago by Bioinfonext120
1

From the manual

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

the basecall phred score, indeed

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by WouterDeCoster36k

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

ADD REPLYlink written 4 weeks ago by Bioinfonext120
2

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).

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by Macspider2.7k
1

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

ADD REPLYlink written 4 weeks ago by finswimmer9.9k

Of course it also depends on the application

ADD REPLYlink written 4 weeks ago by WouterDeCoster36k

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

ADD REPLYlink written 4 weeks ago by lieven.sterck3.9k
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