Which parameters should I use for filtering raw data?

MikeAxtell / ShortStack

ShortStack: Comprehensive annotation and quantification of small RNA genes

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Which parameters should I use for filtering raw data? #63

Closed DiegoZavallo closed 7 years ago

DiegoZavallo commented 7 years ago

Hi Mike, I know that this is not a ShortStack related question (at least not directly), but I was wondering which parameters did you use for small RNA data with Trimmomatic? I only use it for mRNA-Seq data, but when it comes to sRNAs I always used FASTX-Toolkit. Best whishes

Diego

MikeAxtell commented 7 years ago

Hi, somehow I missed this question when you sent it earlier this summer, sorry.

I haven't used trimmomatic. I use cutadapt, with settings

-a [adapter_sequence] --discard-untrimmed -m 16 --max-n=0