A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2025-10-19, 18:00
based on data in:
/home/shared/16TB_HDD_01/graceac9/project-pycno-multispecies-2023/output/28-hisat2-derm-d6-d12
General Statistics
Showing 24/24 rows.| Sample Name | % Aligned |
|---|---|
| PSC-0517-hisat | 87.8% |
| PSC-0523-hisat | 85.4% |
| PSC-0529-hisat | 83.7% |
| PSC-0535-hisat | 88.2% |
| PSC-0547-hisat | 87.0% |
| PSC-0559-hisat | 87.0% |
| PSC-421-hisat | 89.0% |
| PSC-424-hisat | 88.8% |
| PSC-427-hisat | 88.7% |
| PSC-430-hisat | 89.1% |
| PSC-433-hisat | 90.0% |
| PSC-436-hisat | 89.0% |
| PSC-439-hisat | 88.9% |
| PSC-442-hisat | 89.5% |
| PSC-451-hisat | 89.7% |
| PSC-454-hisat | 88.6% |
| PSC-463-hisat | 88.5% |
| PSC-466-hisat | 89.0% |
| PSC-520-hisat | 89.0% |
| PSC-526-hisat | 89.0% |
| PSC-532-hisat | 88.7% |
| PSC-538-hisat | 88.9% |
| PSC-550-hisat | 88.5% |
| PSC-562-hisat | 88.8% |
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.
