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Old 08-27-2018, 06:24 AM   #2
kmcarr
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Location: USA, Midwest

Join Date: May 2008
Posts: 1,172
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Jeff,

Always pre-process read data before downstream analysis. This includes adapter trimming and quality filtering even if you don't expect to find much if any adapter.

As an aside you should perform an additional AmpureXP (or equivalent) clean up on these libraries before sequencing; many contain adapter dimer contamination (the small peak ~130bp). This is especially important if you plan to sequence them on a HiSeq 4000. Even a very small contamination of adapter dimer may produce a significant number of useless reads.
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