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Old 04-25-2018, 05:10 AM   #1
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Default Per base sequence content problem

Hello! I am working with Illumina truseq data. R1 strand looks just fine, however, R2 has a per base sequence content problem
I've done trimming with trimmomatic, here is a screenshot from FastQC.
What is the best strategy to deal with such kind of issue, and what might be the cause? Should I cut everything past 100 nucleotides? Thank you!
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Old 04-25-2018, 05:26 AM   #2
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Do you expect to see those poly-C and poly-T stretches after ~106 position?
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