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Nov 2, 2021 7 tweets 5 min read Read on X
(1/7) A quality control tool for raw #sequence data. Using #FastQC you may check:
🚀 Per base sequence #quality (do you see a drop in sequencing quality near the read end?). This view shows an overview of the range of quality across all bases at each position in the FASTQ file. Per base sequence quality FastQC
(2/7) Per sequence quality scores (how many reads are the best?) The per sequence quality score report shows whether a subset of sequences has universally low-quality values. Per sequence quality scores FastQC
(3/7) Per base sequence content (the proportion of each base position in a file for which each of the four normal #DNA bases has been called). Ideally, in a random library, we would see four parallel lines representing the relative base composition. Per base sequence content FastQC
(4/7) Per sequence GC content (measures the #GC content across the whole length of each sequence). For data of good quality, the graph will show a normal, 🔔bell-shaped distribution. Per sequence GC content
(5/7) Sequence length distribution. This module generates a graph showing the #distribution of #fragment sizes in the file that was analyzed. Some high-throughput #sequencers generate sequence fragments of uniform length, but others can contain #reads of wildly varying lengths. Sequence length distribution FastQC
(6/7) Sequence duplication levels. This module counts the degree of #duplication for every sequence in the set and creates a plot showing the relative number of sequences with different degrees of duplication. A high level of duplication is more likely to indicate enrichment bias Sequence duplication levels FastQC
(7/7) Adapter content (did you remove all #adapters before processing?). The sequence #library adapter sequence is identified at the indicated base position.

bioinformatics.babraham.ac.uk/projects/fastq… Adapter content FastQC

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