Hi,
When Fiber-seq data are aligned to the whole genome, the same genomic region may have different alignments. After using the extract command, different fiber reads can provide different 5mC or m6A modification sites. For example, a genomic position may be covered by 10 reads, but only 3 reads are detected as carrying an m6A modification. Is there an appropriate threshold that can be used to identify reliable or true 5mC or m6A sites? Are there similar approaches or thresholds for MSP and nucleosome (nuc) calls?
Hi,
When Fiber-seq data are aligned to the whole genome, the same genomic region may have different alignments. After using the
extractcommand, different fiber reads can provide different 5mC or m6A modification sites. For example, a genomic position may be covered by 10 reads, but only 3 reads are detected as carrying an m6A modification. Is there an appropriate threshold that can be used to identify reliable or true 5mC or m6A sites? Are there similar approaches or thresholds for MSP and nucleosome (nuc) calls?