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ノート/Trimommaticメモhttp://pepper.is.sci.toho-u.ac.jp/pepper/index.php?%A5%CE%A1%BC%A5%C8%2FTrimommatic%A5%E1%A5%E2 |
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ノート/ノート
訪問者数 1365 最終更新 2017-04-08 (土) 20:37:46
Trimmomatic: A flexible read trimming tool for Illumina NGS data
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: -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