You may wish to keep the (possibly few) long reads which have high quality, instead of clipping them at a fixed length. It is a bit difficult to read the quality boxplot, could you upload it in full resolution?
Did you check for adapter contamination? If you ran FastQC on it, you should get an idea if you have some overrepresented sequences or k-mers in your reads.
Did you check for adapter contamination? If you ran FastQC on it, you should get an idea if you have some overrepresented sequences or k-mers in your reads.
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