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Old 10-06-2016, 06:22 AM   #1
mominchen
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Location: Germany

Join Date: Oct 2016
Posts: 4
Default 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
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Old 10-10-2016, 12:34 AM   #2
Elfangor
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Location: Barcelona

Join Date: Mar 2016
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Default

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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microrna sequencing, trimmomatic

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