A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report generated on 2022-08-11, 11:15 based on data in:
/gscratch/scrubbed/samwhite/outputs/20220810-snam-hisat2-GCF_016432855.1_index-align-stringtie_isoforms
General Statistics
Showing 24/24 rows and 1/1 columns.| Sample Name | % Aligned |
|---|---|
| NPLL32_hisat2.err | 84.2% |
| NPLL34_hisat2.err | 87.2% |
| NPLL44_hisat2.err | 90.2% |
| NPLL46_hisat2.err | 88.2% |
| NPLL56_hisat2.err | 89.8% |
| NPLL61_hisat2.err | 90.6% |
| NPSL15_hisat2.err | 88.0% |
| NPSL24_hisat2.err | 86.4% |
| NPSL29_hisat2.err | 89.9% |
| NPSL36_hisat2.err | 86.8% |
| NPSL50_hisat2.err | 85.9% |
| NPSL58_hisat2.err | 87.1% |
| PLL20_hisat2.err | 89.8% |
| PLL31_hisat2.err | 91.7% |
| PLL43_hisat2.err | 90.7% |
| PLL55_hisat2.err | 71.9% |
| PLL59_hisat2.err | 87.5% |
| PLL62_hisat2.err | 90.6% |
| PSL13_hisat2.err | 90.4% |
| PSL16_hisat2.err | 88.7% |
| PSL35_hisat2.err | 86.7% |
| PSL49_hisat2.err | 84.1% |
| PSL53_hisat2.err | 88.5% |
| PSL63_hisat2.err | 90.7% |
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.
Single-end alignments
This plot shows the number of reads aligning to the reference in different ways.
There are 3 possible types of alignment:
- SE mapped uniquely: Read has only one occurence in the reference genome.
- SE multimapped: Read has multiple occurence.
- SE not aligned: Read has no occurence.
