quality control for 16s metagenome reads

Question

[m90]

Hello everyone,

I have 16S metagenomic reads that are of poor quality. I have attempted to use the fastp tool with various options, but I am still facing issues with dropped tails and unsatisfactory quality scores and GC content. I will provide photos for reference. I would appreciate any help, as I'm unsure about the types of adapters that were used. Note that I am preparing this data for IMNGS. I have also noticed that I have an overrepresentation of reads. Will this negatively impact OTU classification?

Thank you!

 fastp -i step1_clean.fastq.gz -o final_clean.fastq.gz -q 20 -u 30 -n 5 -l 100 -w 4 -h final_fastp.html -j final_fastp.json

[GenoMax]

I have 16S metagenomic reads that are of poor quality.

If true, not much you can do about changing that. Instead of getting stuck on FastQC perhaps start analyzing the data. Join reads/trimming operations that are part of the pipeline like qiime2 can clean up some of the data.

As noted before, if there is a problem with sequencing then talking with the provider may help. If you made the libraries then starting over may be the best option.

Answer 1

[Asaf]

I would have:

1. Discussed it with the sequencing service provider, there might be a problem with the machine (I've never seen such a pattern but I'm no expert)
2. Disregard all the reads from the defective tiles and move forward with the analysis