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FASTQC per base sequence quality FAIL

Hi everybody, I have results of FASTQC and I'm surprised because almost all my samples failed the "per base sequence quality" but it is just the first position in read which values are low. Could you help me, please? Can I continue my RNA-Seq analysis with those results? These are a plot of all results from MultiQC and another oneenter image description here from sample FASTQC:enter image description here

fastqc
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written by irelka.colina • irelka.colina

1 answer

Have you checked the first few reads to see if there is a "N" there, which is likely the dip that you see in cycle 1? It should be fine to proceed with rest of the analysis.

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written by GenoMax GenoMax

Thank you @genomax. I just saw quickly all my fastq.gz files, and the few first reads of forwards files start with an "N".

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written by irelka.colina • irelka.colina

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