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Old 04-27-2016, 04:52 AM   #4
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1. HiSeq 4000 generates optical duplicates (due to pad-hopping). Depending on how you are handling your multi-mappers this could explain the difference.
2. Even though the samples were prepped there is bound to be some rRNA present. You could align to human rDNA repeat independently and see what you get for the two samples as @Chipper suggested.
since mapping is supposed to increase as read length increases
Mapping should become more precise (harder to multi-map) as length increases so that could be another reason for the reduced alignment. You could trim the HiSeq 4000 reads down to 75 bp and see if you get the same ballpark alignment as NextSeq 500 reads.

Last edited by GenoMax; 04-27-2016 at 04:54 AM.
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