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Old 05-16-2020, 01:50 PM   #2
GenoMax
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Location: East Coast USA

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Index sequences are never part of an actual read in Illumina sequencing so you are never going to find index sequences you noted above in R1/R2 reads.

As for the poly-A and ploy-G (no signal, two color chemistry) you just need to remove them during trimming.
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