A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2025-02-14, 10:16 PST
based on data in:
/gscratch/srlab/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/02.20-D-Apul-WGBS-alignment-SLURM_array-bismark
General Statistics
| Sample Name | % Aligned | % Aligned |
|---|---|---|
| 10--1E7-1-bismark | 54.8% | |
| 10--1E7_R1_001 | 58.0% | |
| 1A1-4-bismark | 55.9% | |
| 1A10-2-bismark | 54.6% | |
| 1A10_R1_001 | 56.7% | |
| 1A12-3-bismark | 57.0% | |
| 1A12_R1_001 | 60.5% | |
| 1A1_R1_001 | 59.6% | |
| 1A3-5-bismark | 55.1% | |
| 1A3_R1_001 | 55.8% | |
| 1A5-6-bismark | 57.2% | |
| 1A5_R1_001 | 58.5% | |
| 1A6-7-bismark | 0.2% | |
| 1A6_R1_001 | 60.1% | |
| 1A8-8-bismark | 57.6% | |
| 1A8_R1_001 | 50.5% | |
| 1B1-10-bismark | 55.9% | |
| 1B10-9-bismark | 57.0% | |
| 1B10_R1_001 | 54.9% | |
| 1B1_R1_001 | 59.1% | |
| 1B2-11-bismark | 54.4% | |
| 1B2_R1_001 | 57.6% | |
| 1B4-12-bismark | 0.4% | |
| 1B4_R1_001 | 63.2% | |
| 1B5-13-bismark | 54.0% | |
| 1B5_R1_001 | 60.0% | |
| 1C6-14-bismark | 58.7% | |
| 1C6_R1_001 | 57.6% | |
| 1C8-15-bismark | 56.4% | |
| 1C8_R1_001 | 59.6% | |
| 1C9-16-bismark | 55.1% | |
| 1C9_R1_001 | 60.8% | |
| 1D3-17-bismark | 59.6% | |
| 1D3_R1_001 | 61.7% | |
| 1D7-18-bismark | 57.3% | |
| 1D7_R1_001 | 60.3% | |
| 1D8-19-bismark | 0.2% | |
| 1D8_R1_001 | 57.6% | |
| 1D9-20-bismark | 55.7% | |
| 1D9_R1_001 | 53.0% | |
| 1F1-21-bismark | 58.6% | |
| 1F1_R1_001 | 62.2% | |
| 1F5-22-bismark | 56.0% | |
| 1F5_R1_001 | 59.1% | |
| 1F7-23-bismark | 57.9% | |
| 1F7_R1_001 | 61.8% | |
| 1F9-24-bismark | 0.2% | |
| 1F9_R1_001 | 60.5% | |
| 1G4-25-bismark | 2.3% | |
| 1G4_R1_001 | 2.2% | |
| 1G5-26-bismark | 54.1% | |
| 1G5_R1_001 | 51.0% | |
| 1H11-27-bismark | 52.8% | |
| 1H11_R1_001 | 52.5% | |
| 1H2-28-bismark | 0.4% | |
| 1H2_R1_001 | 53.4% | |
| 1H3-29-bismark | 56.0% | |
| 1H3_R1_001 | 61.5% | |
| 1H5-30-bismark | 0.4% | |
| 1H5_R1_001 | 53.7% | |
| 1H6-31-bismark | 51.1% | |
| 1H6_R1_001 | 54.3% | |
| 1H9-32-bismark | 0.3% | |
| 1H9_R1_001 | 58.3% | |
| 2A3-33-bismark | 54.6% | |
| 2A3_R1_001 | 58.7% | |
| 2C2-34-bismark | 55.6% | |
| 2C2_R1_001 | 55.9% | |
| 2D1-35-bismark | 0.3% | |
| 2D1_R1_001 | 60.8% | |
| 2D2-36-bismark | 54.6% | |
| 2D2_R1_001 | 58.8% | |
| 2G2-37-bismark | 55.3% | |
| 2G2_R1_001 | 60.6% | |
| 2H3-38-bismark | 0.2% | |
| 2H3_R1_001 | 58.7% | |
| 39--2E2-39-bismark | 0.4% | |
| 39--2E2_R1_001 | 58.7% | |
| 6--1E3-40-bismark | 0.3% | |
| 6--1E3_R1_001 | 58.5% |
Bismark
0.24.2
Maps bisulfite converted sequence reads and determine cytosine methylation states.URL: http://www.bioinformatics.babraham.ac.uk/projects/bismarkDOI: 10.1093/bioinformatics/btr167
Alignment Rates
Strand Alignment
Bowtie 2 / HiSAT2
Results from both Bowtie 2 and HISAT2, tools for aligning reads against a reference genome.URL: http://bowtie-bio.sourceforge.net/bowtie2; https://ccb.jhu.edu/software/hisat2DOI: 10.1038/nmeth.1923; 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4
Paired-end alignments
This plot shows the number of reads aligning to the reference in different ways.
There are 6 possible types of alignment:
- PE mapped uniquely: Pair has only one occurence in the reference genome.
- PE mapped discordantly uniquely: Pair has only one occurence but not in proper pair.
- PE one mate mapped uniquely: One read of a pair has one occurence.
- PE multimapped: Pair has multiple occurence.
- PE one mate multimapped: One read of a pair has multiple occurence.
- PE neither mate aligned: Pair has no occurence.
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Software | Version |
|---|---|
| Bismark | 0.24.2 |
