Therefore, some of the sequenced data still remains unclassified (∼14% of total sequenced reads) (Figure 2).
In total, we generated 363 million, 100 bp, single-ended sequenced reads for RRBS experiments.
Using FASTQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), we conducted QC on raw sequenced reads.
(a) Per base sequence content as indicated by FastQC of the raw sequenced reads.
Figure 2: A representative example of signatures and quality of RRBS sequenced reads (sample: X9015).
Sequenced reads were aligned to the mm9 or hg19 reference genome using BSmap32.
The sequenced reads were controlled for quality of sequencing with FastQC tool.
Quality of the sequenced reads for each individual sample was assessed using the FastQC program (see Code availability 1).
The quality of the raw sequenced reads from RNA-Seq experiments was excellent as indicated by FASTQC.
In addition, we do not find substantial differences in the number of sequenced reads and detected genes between samples.
Sequenced reads were aligned to the human genome (GRCh37/hg19) by using Bowtie2 version 2.2.3 and only uniquely mapped reads were used in the subsequent analyses.
