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general:bioseqanalysis:readquality:fastqc [2021/10/20 12:38] – ingogeneral:bioseqanalysis:readquality:fastqc [2021/10/20 12:53] (current) – ingo
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 ====== FASTQC Analysis ====== ====== FASTQC Analysis ======
 So, you will be working with Illumina sequence data, and you are interested in data quality, and particularly in your sequencing error expressed as [[general:bioseqanalysis:sequencequalities|base quality values]]. This is one way to look at the data. So, you will be working with Illumina sequence data, and you are interested in data quality, and particularly in your sequencing error expressed as [[general:bioseqanalysis:sequencequalities|base quality values]]. This is one way to look at the data.
 +<figure FastQC>
 +{{ :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>
  
-  - Identify the read set that you want to analyse. :!: Make sure that you have a 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>