fastqc report of miseq data

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Oct 5, 2016, 2:23:25 AM10/5/16
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Hi everyone,

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.

best regards,


Yoshiki Vázquez Baeza

Oct 5, 2016, 12:41:42 PM10/5/16
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This forum is specific for support related to QIIME, please refer your question to a more general purpose platform like Biostars or SEQanswers.


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