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Fix example for keepBothReads / palindromeKeepBoth #4

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Fix example for keepBothReads / palindromeKeepBoth #4

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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -4,11 +4,11 @@

With most new data sets you can use gentle quality trimming and adapter clipping.

You often don't need leading and traling clipping. Also in general keepBothReads can be useful when working with paired end data, you will keep even redunfant information but this likely makes your pipelines more manageable. Note the additional :2 in front of keepBothReads this is the minimum adapter length in palindrome mode, you can even set this to 1. (Default is a very conservative 8)
You often don't need leading and traling clipping. Also in general keepBothReads can be useful when working with paired end data, you will keep even redundant information but this likely makes your pipelines more manageable. Note the additional :2 in front of keepBothReads is the minimum adapter length in palindrome mode, you can even set this to 1. (Default is a very conservative 8)

If you have questions please don't hesitate to contact us, this is not necessarily one size fits all. (e.g. RNAseq expression analysis vs DNA assembly).

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:keepBothReads LEADING:3 TRAILING:3 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:36


for reference only (less sensitive for adapters)
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