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Old 11-28-2014, 06:53 AM   #9
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Location: Montreal

Join Date: May 2013
Posts: 367

It depends on the type of experiment.

I wouldn't trim for RNA-Seq experiments measuring gene expression levels, or ChIP-Seq experiments measuring immunoprecipitated DNA.
I might trim at 30 or 32 for experiments whose objective is to find mutations (whole-genome seq, exome-seq and sometimes RNA-Seq) or methylation levels (bis-Seq).

For RNA-Seq experiment or ChIP-Seq experiments, trimming would do more harm than good if all your bases are above 25.
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