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*Trimmomaticまとめ 2017-03-31 [#f522fed4]
**Trimmomaticイントロ [#j451ff4b]
[[Trimmomatic: A flexible read trimming tool for Illumina NGS data:http://www.usadellab.org/cms/?page=trimmomatic]]

 java -jar trimmomatic-0.36.jar PE -phred33 input_forward.fq.gz input_reverse.fq.gz
   output_forward_paired.fq.gz output_forward_unpaired.fq.gz
   output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz
   ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

このマシンでは/usr/local/Trimmomatic-0.36に置いたので
 java -jar /usr/local/Trimmomatic/trimmomatic.jar PE -threads 16 -phred33 
  SRR030257_1.fastq SRR030257_2.fastq
  output_forward_paired.fq.gz output_forward_unpaired.fq.gz
  output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz 
  TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
という感じ。あとはパラメタチューニング。

このデータだと
 java -jar /usr/local/Trimmomatic/trimmomatic.jar PE -threads 16 -phred33
   SRR030257_1.fastq SRR030257_2.fastq output_forward_paired.fq.gz
   output_forward_unpaired.fq.gz output_reverse_paired.fq.gz
   output_reverse_unpaired.fq.gz TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
 TrimmomaticPE: Started with arguments:
  -threads 16 -phred33 SRR030257_1.fastq SRR030257_2.fastq
  output_forward_paired.fq.gz output_forward_unpaired.fq.gz
  output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz TRAILING:3
  SLIDINGWINDOW:4:15 MINLEN:36
 Input Read Pairs: 3800180 Both Surviving: 1534275 (40.37%) 
  Forward Only  Surviving: 738222 (19.43%) Reverse Only Surviving: 738370 (19.43%)
  Dropped: 789313 (20.77%)
 TrimmomaticPE: Completed successfully

TRAILING:3だけにすると
 TrimmomaticPE: Started with arguments:
  -threads 16 -phred33 SRR030257_1.fastq SRR030257_2.fastq
    output_forward_paired.fq.gz output_forward_unpaired.fq.gz
    output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz TRAILING:3
 Input Read Pairs: 3800180 Both Surviving: 3800180 (100.00%) 
  Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 0 (0.00%)
   Dropped: 0 (0.00%)
 TrimmomaticPE: Completed successfully

Trailing:20にすると
TrimmomaticPE: Started with arguments:
  TrimmomaticPE: Started with arguments:
  -threads 16 -phred33 SRR030257_1.fastq SRR030257_2.fastq
   output_forward_paired.fq.gz output_forward_unpaired.fq.gz
   output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz TRAILING:20
 Input Read Pairs: 3800180 Both Surviving: 3666565 (96.48%)
   Forward Only Surviving: 133611 (3.52%) Reverse Only Surviving: 1 (0.00%)
   Dropped: 3 (0.00%)
 TrimmomaticPE: Completed successfully

Trailing:20でSlidingWindow:4:15にしてみると
 TrimmomaticPE: Started with arguments:
   -threads 16 -phred33 SRR030257_1.fastq SRR030257_2.fastq
   output_forward_paired.fq.gz output_forward_unpaired.fq.gz
   output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz TRAILING:20
   SLIDINGWINDOW:4:15
 Input Read Pairs: 3800180 Both Surviving: 3655255 (96.19%)
   Forward Only Surviving: 144886 (3.81%) Reverse Only Surviving: 19 (0.00%)
   Dropped: 20 (0.00%)
 TrimmomaticPE: Completed successfully

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