Trimmomatic parameters

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2.3 years ago

ronny • 0

$java -jar /apps/eb/Trimmomatic/0.39-Java-1.8.0_144/trimmomatic-0.39.jar PE -phred33 seq1_L2_1.fq.gz seq1_L2_2.fq.gz _L2_r1_paired_fq.gz seq1_L2_r1_unpaired.fq.gz seq_L2_r2_paired.fq.gz Seq1_L2_r2_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:5

what values I should use for following parameters?

ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:5

Trimmomatic • 1.0k views

ADD COMMENT • link updated 2.3 years ago by GenoMax 141k • written 2.3 years ago by ronny • 0

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Hi ronny, without additional information about your libraries and quality of your data, this will be a difficult question to answer. I would first suggest generating FastQC/MultiQC reports. This should help you get an idea about the values for each of the parameters that are right for your data. Good luck!

ADD REPLY • link 2.3 years ago by Chris Dean ▴ 390

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Thank you Chris Dean , I did FastQC.

ADD REPLY • link 2.3 years ago by ronny • 0

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