bbduk trimmed out too many sequences


Hi all,

I'm trying to use to trim out my 16S V4 primer sequences from my samples using command below. in1=${SAMPLE}_R1_001.fastq.gz in2=${SAMPLE}_R2_001.fastq.gz 
        out1=ra_${SAMPLE}_R1.fastq out2=ra_${SAMPLE}_R2.fastq 
        ktrim=l k=20 mink=19 copyundefined=t 
        literal="GTGCCAGCMGCCGCGGTAA,GGACTACHVGGGTWTCTAAT" hdist=1 stats=${SAMPLE}_stats.txt 
        tpe tbo

But from the result, it trimmed out most of the reads (around 90%). I then tried to use another tool cutadapt to check and it gives a totally different results.

At first I thought there was something wrong with the sequencing run but since cutadapt is able to retain most of the reads, I believe there is something wrong with my command above.

Really appreciate if anyone can help me on this. I spent too much time checking this issue now lol.
Thank you in advance.





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