multiqc report, should I care for "Per Base Sequence Content" module if using metagenomic datasets?
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14 months ago

Hello I ran fastqc and later multiqc for parsing my metagenomic files, and on the Per Base Sequence Content module all my files are marked with red (i.e they failed the analysis) should I really take care of this given the fact that I'm using metagenomic datasets?.

fastqc multiqc • 704 views
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Show us what the plot looks like.

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In many cases, the answer to this is "no". See positional sequence bias in randomly primed libraries, though of course this depends on your library prep and may not apply in this case.

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