What is --trimmomatic default parameters

[Farbod Emami]

Dear Brian , Hi

When using "--trimmomatic" in the standard Trinity paired end assembly script, what default parameters of this program will run? as it seems that Trimommatic is flexible in the field of Phred score and Adapter removing.

Thanks

  

[Brian Haas]

It's shown under Trinity --show_full_usage_info

#### Quality Trimming Options ####  

# 

#  --quality_trimming_params <string>   defaults to: "ILLUMINACLIP:trinityrnaseq/trinity-plugins/Trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25"

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Brian J. Haas
The Broad Institute
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[Farbod Emami]

Dear Brian, Hi

It seems that there is no phred quality score trimming or "N" nucleotide trimming in this default , am I right ?

On Sunday, November 1, 2015 at 2:47:32 AM UTC+3:30, Brian Haas wrote:

It's shown under Trinity --show_full_usage_info

#### Quality Trimming Options ####  

# 

#  --quality_trimming_params <string>   defaults to: "ILLUMINACLIP:trinityrnaseq/trinity-plugins/Trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25"

On Sat, Oct 31, 2015 at 6:06 PM, Farbod Emami <farbo...@gmail.com> wrote:

Dear Brian , Hi

When using "--trimmomatic" in the standard Trinity paired end assembly script, what default parameters of this program will run? as it seems that Trimommatic is flexible in the field of Phred score and Adapter removing.

Thanks

  

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[Matthew MacManes]

it’s SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5

Trimming PHRED < 5 from both ends and sliding window.

______________________________________________
Matthew MacManes, Ph.D.
University of New Hampshire  I  Assistant Professor of Genome Enabled Biology
Department of Molecular, Cellular, & Biomedical Sciences
Durham, NH  03824
Phone: 603-862-4052  I  Twitter: @macmanes | Web: genomebio.org
Office: 189 Rudman Hall | Laboratory: 145 Rudman Hall

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[Farbod Emami]

Dear Matthew, Hi and thank you,

I usually have heard about PHRED quality score = 20 and = 30 , whould you please tell me what this <5 score mean ?

[Matthew MacManes]

By <5 I mean that you will only trim bases where the quality is less than Phred5. Trimming at a Phred score as high as 20 or 30 is likely limiting the quality of your assembly. See http://www.ncbi.nlm.nih.gov/pubmed/24567737

Matt

______________________________________________
Matthew MacManes, Ph.D.
University of New Hampshire  I  Assistant Professor of Genome Enabled Biology
Department of Molecular, Cellular, & Biomedical Sciences
Durham, NH  03824
Phone: 603-862-4052  I  Twitter: @macmanes | Web: genomebio.org
Office: 189 Rudman Hall | Laboratory: 145 Rudman Hall

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[Tiago Hori]

I always forget about that trimming paper. It is awesome!

T.

"Profanity the is the only language all programmers understand" 

Sent from my iPhone, the universal excuse for my poor spelling.