It has been proposed that this specificity is due to the unique alignment of the monoalkylated guanine in the minor groove, and is not affected by the surrounding nucleotide context (Sastry et al. 1995; Gargiulo et al. 1995).
Direct alignment of the 35 bp Illumina reads resulted in the unique alignment of approximately one-third of the sequences.
For instance, features such as the presence of repetitive DNA make the unique alignment of sequence reads difficult or impossible.
We used the appropriate arguments to allow up to two mismatches per read with no gaps, and to report the unique alignment with the least number of mismatches.
Identification of M regions is performed after discarding the unique alignments from total alignments.
Each aligned read was assigned a mapping quality that indicates whether the read has a unique alignment or can be aligned to multiple positions in the genome [ 22].
Using this database, we successfully identified unique alignment positions for 51 of 436 sequenced RAD loci (11.0%).
This bisulfate mapping tool aims to find unique alignment through running four alignment processes simultaneously (Krueger and Andrews, 2011).
For gene expression analysis, we only examined transcripts with a reciprocal hit in the other genotype where >75% of the aligned reads were unique alignments, not aligning to any other transcripts.
