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  • Trimmomatic settings for miRNA

    Hello everyone,
    I hope to find someone who can help. I want to use trimmomatic for single end Illumina reads from miRNA sequencing. I'm specifically unsure about the parameters: SLIDINGWINDOW and ILLUMINACLIP. I'm open to any suggestions, because I'm totally new to miRNA seq. RNA-seq I did before.

    Code:
    -threads 1 
    -phred33 #encoding Sanger / Illumina 1.9
    ILLUMINACLIP:./adapters/list.fa:2:30:10:6 
    LEADING:3 
    TRAILING:3 
    SLIDINGWINDOW:4:15 
    MINLEN:17"
    I really would appriciate your suggestions for this. Thanks

  • #2
    I work on miRNA-seq and I've used the software Cutadapt for trimming adapters. Have a look to it, I find it quite usefull and simpler.

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