User: annsun89

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annsun8910
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Posts by annsun89

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Answer: A: Trimmomatic adapter clipping removes many reads even if "keepBothReads" paramete
... Hi, I read the manual and is the name of the parameter but it's not how to set it. Instead, try java -jar trimmomatic-0.33.jar PE R1.fastq.gz R2.fastq.gz PR1.fastq.gz UPR1.fastq.gz PR2.fastq.gz UPR2.fastq.gz ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:1:TRUE ...
written 4 months ago by annsun8910
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Comment: C: Leftover adapter sequences after Trimmomatic trimming?
... Ah, thank you very much, both for the answer and for the extra help! I will try bbduk.sh and see how it goes. I used trimmomatic because it was a tool already available on the cloud cluster I'm using (compute canada). However, is there a specific reason to use bbduk.sh instead of trimmomatic other ...
written 4 months ago by annsun8910
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Leftover adapter sequences after Trimmomatic trimming?
... Hi everyone, I'm a wet lab biologist who now has 100+ RNA-seq samples to analyze so it's been a steep learning curve. Any help would be super appreciated! I have PE 125bp fastq files from an Illumina Hiseq and my fastqc analysis shows Illumina Universal Adapter contamination. I used trimmomatic t ...
trimmomatic adapters trimming rna-seq written 4 months ago by annsun8910 • updated 4 months ago by genomax58k

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Scholar 4 months ago, created an answer that has been accepted. For A: Trimmomatic adapter clipping removes many reads even if "keepBothReads" paramete

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