A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2025-10-15, 12:33
based on data in:
/home/shared/16TB_HDD_01/graceac9/project-pycno-multispecies-2023/output/27-hisat2-pisaster-d6-d12
General Statistics
Showing 24/24 rows.| Sample Name | % Aligned |
|---|---|
| PSC-0518-hisat | 86.5% |
| PSC-0524-hisat | 85.0% |
| PSC-0530-hisat | 85.9% |
| PSC-0536-hisat | 85.0% |
| PSC-0548-hisat | 86.6% |
| PSC-0560-hisat | 83.8% |
| PSC-422-hisat | 87.7% |
| PSC-425-hisat | 86.3% |
| PSC-428-hisat | 86.0% |
| PSC-431-hisat | 88.0% |
| PSC-434-hisat | 86.5% |
| PSC-437-hisat | 85.4% |
| PSC-440-hisat | 87.0% |
| PSC-443-hisat | 83.4% |
| PSC-452-hisat | 85.5% |
| PSC-455-hisat | 88.4% |
| PSC-464-hisat | 87.8% |
| PSC-467-hisat | 88.7% |
| PSC-521-hisat | 85.3% |
| PSC-527-hisat | 87.4% |
| PSC-533-hisat | 85.3% |
| PSC-539-hisat | 82.9% |
| PSC-551-hisat | 86.3% |
| PSC-563-hisat | 86.9% |
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.
