Dear all, long time listener first time caller here.
I've got some Agilent Methyl-Seq data, I'm looking for feedback from anyone with experience with this data - i.e. enrichment for regions of interest, then BS then sequencing. I've been using Bismark (great!, thanks very much Babraham!) and have just given Trim Galore! a whirl. Any tips on parameters used, trimming etc, I've only got about 66% mapping efficiency and would like to improve upon that.
thanks.
I've got some Agilent Methyl-Seq data, I'm looking for feedback from anyone with experience with this data - i.e. enrichment for regions of interest, then BS then sequencing. I've been using Bismark (great!, thanks very much Babraham!) and have just given Trim Galore! a whirl. Any tips on parameters used, trimming etc, I've only got about 66% mapping efficiency and would like to improve upon that.
thanks.
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