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general:bioseqanalysis:readquality:fastqc [2021/10/20 12:50] – ingogeneral:bioseqanalysis:readquality:fastqc [2021/10/20 12:53] (current) – ingo
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 <figure FastQC> <figure FastQC>
 {{ :general:bioseqanalysis:images:fastqc.png?600 |}} {{ :general:bioseqanalysis:images:fastqc.png?600 |}}
 +<caption><fs 0.8em>Example output of a FASTQC analysis taken from the [[https://www.bioinformatics.babraham.ac.uk/projects/fastqc/|software homepage]]</fs></caption>
 </figure> </figure>
  
-  - Identify the read set that you want to analyse. :!: Make sure that you have a [[general:bioseqanalysis:formats:fastq|fastq]] format<WRAP>+  - Identify the read set that you want to analyse. :!: Make sure that you have a [[general:bioseqanalysis:sequencequalities#storing_base_quality_information|fastq]] format<WRAP>
 <hidden PairedEndLayout>In the case you are having a paired end library layout, is convention that you analyse forward and reverse reads separately, since their quality typically varies considerably. You can use samtools to split your readset into forward and reverse reads in the case you are having both in one file <hidden PairedEndLayout>In the case you are having a paired end library layout, is convention that you analyse forward and reverse reads separately, since their quality typically varies considerably. You can use samtools to split your readset into forward and reverse reads in the case you are having both in one file
 </hidden> </hidden>