gravatar for Apprentice

6 hours ago by


I'm using Trimmomatic v0.39 to trim low quality base.
I set MINLEN option to 50 as below.

java -Xmx4g -jar trimmomatic-0.39.jar PE 
-threads 1 -phred33 -trimlog ${id}.trimlog 
${id}_R1.paired.fastq.gz ${id}_R1.unpaired.fastq.gz 
${id}_R2.paired.fastq.gz ${id}_R2.unpaired.fastq.gz 

However, trimmed fastq file had reads with length<50.
I thought it might be dropped if both reads are less than MINLEN in length in the case of paired end. In other words, if one read length is less than MINLEN, but the other read is longer than MINLEN, it will not be dropped.
Is this idea correct?

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