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I am checking the quality control of my sequences using the Fastqc tool. For some steps, like "Per base GC content", etc., I received a warning. So, I was wondering whether I Should also take care of warning messages in the Fastqc tool or I should only care about errors! I would appreciate it if someone could help me with this, please.

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  • $\begingroup$ Whether the warning is heeded or not it all depends on the kind of data you are working on and the type of analysis you should be doing. If you could tell us a little bit about what you are working on and what kind of analysis you want to do that could help us $\endgroup$
    – Diango
    Mar 31 '20 at 9:24
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Generally yes, but it depends the type of study. Remember that Fastqc was developed for bacterial genomes, mainly, so an unusually shaped distribution in that particular dataset could indicate a contaminated library. But, for example, in an amplicon 16S amplicon dataset it's expected that other modules fail (Duplicate Sequences, Overrepresented Sequences, etc.) not only GC.

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  • $\begingroup$ Maybe, it is good to mention that I am working on the genomic data of E. Coli. So, in this case, you believe that the warnings are also important, right? $\endgroup$
    – Negin
    Mar 24 '20 at 13:00
  • $\begingroup$ According to the documentation "A warning is raised if the sum of the deviations from the normal distribution represents more than 15% of the reads... usually indicate a problem with the library". You need to check in the downstream analysis if you have adapters, or other kind of contamination. $\endgroup$
    – zorbax
    Mar 24 '20 at 13:14

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