Remove leading low quality or N bases (below quality 3) (LEADING:3).Remove adapters (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10).Java -jar trimmomatic-0.35.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 Java -jar trimmomatic-0.39.jar PE 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:2:30:10:2:True LEADING:3 TRAILING:3 MINLEN:36įor reference only (less sensitive for adapters) RNAseq expression analysis vs DNA assembly). If you have questions please don't hesitate to contact us, this is not necessarily one size fits all. Note the additional :2 in front of True (for keepBothReads) this is the minimum adapter length in palindrome mode, you can even set this to 1. Also in general setting keepBothReads to True can be useful when working with paired end data, you will keep even redunfant information but this likely makes your pipelines more manageable. You often don't need leading and traling clipping. With most new data sets you can use gentle quality trimming and adapter clipping. Version 0.36: binary and source Quick start Paired End: Starting on version 0.40 we also offer a github page (as well as older versions) Trimmomatic: A flexible trimmer for Illumina Sequence Data. Trimmomatic: A flexible read trimming tool for Illumina NGS dataīolger, A.
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