CpG_Me
QC for a custom WGBS workflow
Multiple QC reports summarise filtering, trimming, alignment, and methylation bias (m-bias) results.
This is the LaSalle lab version of CpG_Me for single end sequencing.
- Workflow Developer
- Ben Laufer
- blaufer@ucdavis.edu
- Application Type
- WGBS
- Project Type
- Down Syndrome
- Sequencing Platform
- HiSeq 2000
- Sequencing Setup
- SE 100 SI
- Library Kit
- MethylC-seq
- Genome
- hg38
Report generated on 2018-06-03, 11:03 based on data in:
/share/lasallelab/Ben/DownSyndrome/Update
General Statistics
Showing 9/9 rows and 8/13 columns.| Sample Name | % mCpG | M C's | C Coverage | % Dups | M Unique | M Aligned | % Aligned | % Trimmed |
|---|---|---|---|---|---|---|---|---|
| JLKD062_filtered | 76.2% | 1630.4 | 2.60X | 6.4% | 119.5 | 127.7 | 71.1% | 15.5% |
| SRR3536978 | 76.8% | 1566.2 | 2.50X | 6.0% | 114.9 | 122.2 | 74.3% | 1.7% |
| SRR3536980 | 77.2% | 1561.4 | 2.49X | 4.1% | 118.1 | 123.2 | 72.0% | 1.6% |
| SRR3537005 | 74.0% | 1181.2 | 1.89X | 4.6% | 99.0 | 103.7 | 71.8% | 2.3% |
| SRR3537006 | 78.4% | 1502.1 | 2.40X | 5.4% | 108.5 | 114.7 | 75.2% | 1.5% |
| SRR3537007 | 78.1% | 1540.2 | 2.46X | 4.1% | 121.3 | 126.5 | 72.9% | 2.0% |
| SRR3537008 | 74.8% | 434.7 | 0.69X | 17.8% | 28.0 | 34.1 | 77.3% | 2.1% |
| SRR3537015 | 74.8% | 1014.4 | 1.61X | 4.8% | 82.3 | 86.4 | 56.6% | 2.0% |
| SRR3537016 | 76.8% | 1020.9 | 1.62X | 3.5% | 81.2 | 84.1 | 59.0% | 1.7% |
Bismark
Bismark is a tool to map bisulfite converted sequence reads and determine cytosine methylation states.
Alignment Rates
Deduplication
Strand Alignment
All samples were run with --directional mode; alignments to complementary strands (CTOT, CTOB) were ignored.
Cytosine Methylation
M-Bias
This plot shows the average percentage methylation and coverage across reads. See the bismark user guide for more information on how these numbers are generated.
FastQ Screen
FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.
FastQC
FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.
Sequence Quality Histograms
The mean quality value across each base position in the read. See the FastQC help.
Per Sequence Quality Scores
The number of reads with average quality scores. Shows if a subset of reads has poor quality. See the FastQC help.
Per Base Sequence Content
The proportion of each base position for which each of the four normal DNA bases has been called. See the FastQC help.
Rollover for sample name
Per Sequence GC Content
The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content. See the FastQC help.
Per Base N Content
The percentage of base calls at each position for which an N was called. See the FastQC help.
Sequence Length Distribution
The distribution of fragment sizes (read lengths) found. See the FastQC help.
Sequence Duplication Levels
The relative level of duplication found for every sequence. See the FastQC help.
Overrepresented sequences
The total amount of overrepresented sequences found in each library. See the FastQC help for further information.
Adapter Content
The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. See the FastQC help. Only samples with ≥ 0.1% adapter contamination are shown.
Cutadapt
Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.
This plot shows the number of reads with certain lengths of adapter trimmed. Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length. See the cutadapt documentation for more information on how these numbers are generated.
