Hi Sagun,
Thank you for your answer. The code I used for paired-end reads as below:
"kneaddata --input R1.fastq --input R2.fastq --output kneaddata_output --bowtie2 database_folder --trimmomatic-options “SLIDINGWINDOW:4:20 MINLEN:60”. For example, if the MINLEN is set to 60, all the samples in the log file will show MINLEN 60. May I ask why?
When I run with the default, I found that the MINLEN number in the log file is different across samples. I think this is correct as you said “MINLEN is computed each time” for each sample, right?
Thanks.
Wang