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It could also be rRNA; what does the GC plot (per sequence GC content) look like?
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The problem that you describe in the first few bases is often seen with RNA-Seq data,
and is thought to be due to the random priming being not so random in practice.
This has previously been disussed in various threads, one of which is here:
The trimmomatic adapter trimming only trims adapter sequences from the 3' ends of the reads.Comment
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Thanks for all the answers!!! and the link
sarvidsson: The GC plot looks terrible there are 3 peaks in the reads is not a normal distribution.Comment
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