Hi all,

I am working on 16S rRNA sequence of anaerobes enriched from wastewater treatment plant.

I was trying to do some genome binning but it was unsuccessful, so I went back to do some trimmomatic and QC, I found that although the sequence quality improved, my per base sequence content is always a fail, also the per tile sequence quality becomes worse than the untrimmed sequence file.

the code I ran was:

trimmomatic PE -threads 4 -phred 33 \ Raw160823_1.fastq.gz Raw160823_2.fastq.gz \ Raw160823_1_trimmed.fastq.gz Raw160823_1_trimmed_failed.fastq.gz Raw160823_2_trimmed.fastq.gz Raw160823_2_trimmed_failed.fastq.gz \ HEADCROP:10 TRAILING:10 SLIDINGWINDOW:4:30 MINLEN:80

I have tried changing the value of the parameters but the results were about the same. What do you all think? Do I have to make sure all the checks are passed before I proceed to assembly, or do I just care about the per base sequence quality?

Thank you, Kai