I have a confusion regarding human metagenomic sample (MiSeq) and hope to get some help from this forum.
I have performed RNAseq gene expression data analysis before and there I would do the quality checking with Fastqc.
Now, the confusion arises here -
I recently got into analyzing human metagenomic sample. Following the same quality check step using Fastqc, I get really bad report and I am very doubtful about getting trustworthy results out of this data. I discussed this with my colleague biologists (who too are new in this field), they said its should be okay to carry on analysis with this data. So, I decided to ask the community for suggestions. I have attached the fastqc report for paired end reads. I would appreciate if anyone could spare some time to have a look on the report and see if it is sensible to analyze that data.