Table 1 The main output files in each step of the MethyQA pipeline

SampleName_fastqc

Step 1

One folder and one zip file that save the output of quality assessment using fastqc.

SampleName_fastqc.zip

fastx.trim.fastq

Step 2

Fastx or cutadapt output (one line per read) if adapter trimming is used.

cutadapt.trim.fastq

*_reads1.txt

Step 2

BRAT trimming output (one line per read) if dynamic trimming using BRAT trim is done.

fixedTrim_BRATout

Step 2

Fixed length trimming output (one line per read) if “fixed-length” trimming is used.

alignment.brat

Step 3

BRAT alignment output (one line per read).

* _forw.txt

Step 3

BRAT ACGT-count (i.e., methylation ratio) output file (one line per cytosine position).

*chrN.summary.table.txt

Step 4

Chromosome level summary table for bisulfite conversion rates.

*chrN.BS.ps

Step 4

Chromosome level plot for bisulfite conversion rates.

*chrN.target.summary.table.txt

Step 4

Target region level summary table for the mean and median of bisulfite conversion rates.

*chrN.mean.median.ps

Step 4

Target region level plot for the mean and median of bisulfite conversion rates.

*chrN.seq.bisulfite.boxplot.ps

Step 5

Plots for comparing the DNA sequence structure for regions with high and low bisulfite conversion rates.

*chrN.highBS.seq

Step 5

Target regions with high or low bisulfite conversion rates (*seq files include all basic DNA sequence statistics, and *target files include the summary of nonCGc bisulfite conversion rates).

*chrN.lowBS.seq

*chrN.highBS.target

*chrN.lowBS.target

*chrN.seq.coverage.boxplot.ps

Step 5

Plots for comparing the DNA sequence structure for regions with high and low sequencing coverage.

*chrN.highCoverage.seq

Step 5

Target regions with high or low sequencing coverage (*seq files include all basic DNA sequence statistics, and *target files include the summary of nonCGc bisulfite conversion rates).

*chrN.lowCoverage.seq

*chrN.highCoverage.target

*chrN.lowCoverage.target