From: MethyQA: a pipeline for bisulfite-treated methylation sequencing quality assessment
File name | Pipeline step | Descriptions |
---|---|---|
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 |