Fig. 3
From: Software updates in the Illumina HiSeq platform affect whole-genome bisulfite sequencing
Quality scores assigned to base G. a Quality scores assigned to Gs in the raw reads obtained using different HCS versions. All Gs were grouped into four classes according to the assigned quality score. b Examples of drops in quality score at Gs. Representative sequence reads from the PBAT-seq (IMR-90) and control (PhiX) data generated using HCS v2.0.12 are shown. Gs in the IMR-90 read are shown in red. c Quality scores assigned to the base representing 5mC (G or C) in R1 and R2 of the paired-end PBAT-seq and MethylC-seq using HCS v2.0.12. In the MethylC-seq, 50% w/w PhiX DNA was spiked in (accession no. DRA002280) [14]