A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report generated on 2020-11-30, 17:24 based on data in:
/share/workshop/epigenetics_workshop/jli/Methylation/03-Bismark/SRR9833662.1.inputSRR9833662.1_R1_001_bismark_bt2_pe.deduplication_report.txt
/share/workshop/epigenetics_workshop/jli/Methylation/03-Bismark/SRR9833662.1.inputSRR9833662.1_R1_001_bismark_bt2_PE_report.txt
/share/workshop/epigenetics_workshop/jli/Methylation/03-Bismark/SRR9833663.inputSRR9833663_R1_001_bismark_bt2_pe.deduplication_report.txt
/share/workshop/epigenetics_workshop/jli/Methylation/03-Bismark/SRR9833663.inputSRR9833663_R1_001_bismark_bt2_PE_report.txt
/share/workshop/epigenetics_workshop/jli/Methylation/03-Bismark/SRR9833664.inputSRR9833664_R1_001_bismark_bt2_pe.deduplication_report.txt
/share/workshop/epigenetics_workshop/jli/Methylation/03-Bismark/SRR9833664.inputSRR9833664_R1_001_bismark_bt2_PE_report.txt
/share/workshop/epigenetics_workshop/jli/Methylation/03-Bismark/SRR9833670.1.inputSRR9833670.1_R1_001_bismark_bt2_pe.deduplication_report.txt
/share/workshop/epigenetics_workshop/jli/Methylation/03-Bismark/SRR9833670.1.inputSRR9833670.1_R1_001_bismark_bt2_PE_report.txt
/share/workshop/epigenetics_workshop/jli/Methylation/03-Bismark/SRR9833671.inputSRR9833671_R1_001_bismark_bt2_pe.deduplication_report.txt
/share/workshop/epigenetics_workshop/jli/Methylation/03-Bismark/SRR9833671.inputSRR9833671_R1_001_bismark_bt2_PE_report.txt
/share/workshop/epigenetics_workshop/jli/Methylation/03-Bismark/SRR9833672.inputSRR9833672_R1_001_bismark_bt2_pe.deduplication_report.txt
/share/workshop/epigenetics_workshop/jli/Methylation/03-Bismark/SRR9833672.inputSRR9833672_R1_001_bismark_bt2_PE_report.txt
/share/workshop/epigenetics_workshop/jli/Methylation/04-Methylation/SRR9833662.1.inputSRR9833662.1_R1_001_bismark_bt2_pe.deduplicated.M-bias.txt
/share/workshop/epigenetics_workshop/jli/Methylation/04-Methylation/SRR9833663.inputSRR9833663_R1_001_bismark_bt2_pe.deduplicated.M-bias.txt
/share/workshop/epigenetics_workshop/jli/Methylation/04-Methylation/SRR9833664.inputSRR9833664_R1_001_bismark_bt2_pe.deduplicated.M-bias.txt
/share/workshop/epigenetics_workshop/jli/Methylation/04-Methylation/SRR9833670.1.inputSRR9833670.1_R1_001_bismark_bt2_pe.deduplicated.M-bias.txt
/share/workshop/epigenetics_workshop/jli/Methylation/04-Methylation/SRR9833671.inputSRR9833671_R1_001_bismark_bt2_pe.deduplicated.M-bias.txt
/share/workshop/epigenetics_workshop/jli/Methylation/04-Methylation/SRR9833672.inputSRR9833672_R1_001_bismark_bt2_pe.deduplicated.M-bias.txt
/share/workshop/epigenetics_workshop/jli/Methylation/04-Methylation/SRR9833662.1.inputSRR9833662.1_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt
/share/workshop/epigenetics_workshop/jli/Methylation/04-Methylation/SRR9833663.inputSRR9833663_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt
/share/workshop/epigenetics_workshop/jli/Methylation/04-Methylation/SRR9833664.inputSRR9833664_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt
/share/workshop/epigenetics_workshop/jli/Methylation/04-Methylation/SRR9833670.1.inputSRR9833670.1_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt
/share/workshop/epigenetics_workshop/jli/Methylation/04-Methylation/SRR9833671.inputSRR9833671_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt
/share/workshop/epigenetics_workshop/jli/Methylation/04-Methylation/SRR9833672.inputSRR9833672_R1_001_bismark_bt2_pe.deduplicated_splitting_report.txt
General Statistics
Showing 6/6 rows and 4/6 columns.Sample Name | % mCpG | M C's | % Dups | % Aligned |
---|---|---|---|---|
SRR9833662.1.inputSRR9833662.1_R1_001 | 83.1% | 141.6 | 4.0% | 100.0% |
SRR9833663.inputSRR9833663_R1_001 | 83.4% | 150.8 | 3.7% | 100.0% |
SRR9833664.inputSRR9833664_R1_001 | 82.9% | 156.4 | 3.7% | 100.0% |
SRR9833670.1.inputSRR9833670.1_R1_001 | 83.3% | 124.5 | 3.8% | 100.0% |
SRR9833671.inputSRR9833671_R1_001 | 82.3% | 138.5 | 3.4% | 100.0% |
SRR9833672.inputSRR9833672_R1_001 | 82.4% | 135.6 | 3.5% | 100.0% |
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.