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We could observe that "Per base sequence quality" figure (to the left) is better in comparison to the figure before trimming. Some of the reads with quality lower than 20 were excluded from the analysis, especially that at the end of reads (46-50 base pair). Similar changes can also be seen at "Sequence length (bp)" figure before and after trimming (to the right). The main part of reads remained without trimming (50 bp) but from some of them adapters (probably those which lower than 45 bp) and reads which have poor quality (46-49 bp) were cut off. The middle figure, "Per base sequence content" shows the mean percentage of nucleotides (A, C, G, T). We could observe that after trimming, mainly of adapters which have repetitive sequences, there was equalization of the mean nucleotide percentage in comparison to reads before trimming.

Closing remarks

This tutorial covers trimming adapters and low quality reads using Flexbar. Additionally, we used FastQC at every step of analysis to control quality of our raw reads. It should be the first step before you proceed with the alignment of your raw sequences to the reference Short reads alignment to human reference genome using BWA or Short reads alignment to mouse transcriptome using Tophat2