Adaptor trimming for TruSeq DNA Methylation

1.

TruSeq DNA Methylation所使用的adapter序列與 TruSeq Single Index系統相同， bcl2fastq v2.2 guide在拆分過程中該軟體判斷adapter序列的嚴謹度(adapter stringency)定義如下：

The minimum match rate that triggers masking or trimming. This value is calculated as MatchCount / (MatchCount + MismatchCount). … The default value of 0.9 indicates that only reads with > 90% sequence identity with the adapter are trimmed.

(page. 14, bcl2fastq2-v2-20-software-guide)

由此研判，
25 mer 需有 23 mer 符合分析者給予的序列 (92%)
33 mer 需有 30 mer 符合分析者給予的序列 (90.9%)
才會被trim，兩者比例僅些微差異。

2.

起初由於TruSeq DNA Methylation的建議讀長較短( 2×75 or 2×100bp)，作為因應，提供的trimming序列亦較短；若使用較長的讀長如2×150或以上，亦可以使用33 mer；但整體而言，25 mer就可以達到trim adapter的效果。
Recommended read length: TruSeq DNA Methylation (illumina.com)