A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2024-06-18, 10:45
based on data in:
/home/shared/8TB_HDD_02/graceac9/GitHub/paper-pycno-sswd-2021-2022/analyses/03-hisat2
General Statistics
Showing 32/32 rows.| Sample Name | % Aligned |
|---|---|
| PSC-19-hisat | 81.5% |
| PSC-23-hisat | 79.2% |
| PSC-24-hisat | 74.6% |
| PSC-34-hisat | 10.3% |
| PSC-35-hisat | 16.1% |
| PSC-36-hisat | 24.3% |
| PSC-37-hisat | 10.2% |
| PSC-38-hisat | 11.5% |
| PSC-39-hisat | 15.0% |
| PSC-40-hisat | 13.9% |
| PSC-42-hisat | 80.3% |
| PSC-43-hisat | 81.9% |
| PSC-48-hisat | 78.3% |
| PSC-49-hisat | 77.7% |
| PSC-52-hisat | 79.5% |
| PSC-54-hisat | 80.3% |
| PSC-56-hisat | 74.9% |
| PSC-57-hisat | 83.4% |
| PSC-58-hisat | 80.2% |
| PSC-59-hisat | 78.1% |
| PSC-61-hisat | 78.8% |
| PSC-63-hisat | 80.5% |
| PSC-64-hisat | 80.7% |
| PSC-67-hisat | 77.4% |
| PSC-69-hisat | 78.0% |
| PSC-71-hisat | 77.8% |
| PSC-73-hisat | 79.4% |
| PSC-75-hisat | 46.6% |
| PSC-76-hisat | 79.1% |
| PSC-78-hisat | 63.4% |
| PSC-81-hisat | 77.7% |
| PSC-83-hisat | 81.6% |
Bowtie 2 / HiSAT2
Bowtie 2 and HISAT2 are fast and memory-efficient tools for aligning sequencing reads against a reference genome. Unfortunately both tools have identical log output by default, so it is impossible to distiguish which tool was used. .DOI: 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.
