A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2024-10-10, 20:50 PDT
based on data in:
/home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/02.20-D-Apul-RNAseq-alignment-HiSat2
General Statistics
Showing 80/80 rows and 2/4 columns.| Sample Name | M Reads Mapped | % Aligned |
|---|---|---|
| 1A1-hisat2_output | 37.0 | |
| 1A10-hisat2_output | 36.5 | |
| 1A10_hisat2 | 70.7% | |
| 1A12-hisat2_output | 32.7 | |
| 1A12_hisat2 | 79.8% | |
| 1A1_hisat2 | 71.7% | |
| 1A2-hisat2_output | 36.8 | |
| 1A2_hisat2 | 71.4% | |
| 1A8-hisat2_output | 30.5 | |
| 1A8_hisat2 | 75.0% | |
| 1A9-hisat2_output | 36.3 | |
| 1A9_hisat2 | 72.3% | |
| 1B1-hisat2_output | 37.6 | |
| 1B10-hisat2_output | 38.1 | |
| 1B10_hisat2 | 79.4% | |
| 1B1_hisat2 | 75.4% | |
| 1B2-hisat2_output | 37.0 | |
| 1B2_hisat2 | 75.4% | |
| 1B5-hisat2_output | 41.3 | |
| 1B5_hisat2 | 80.2% | |
| 1B9-hisat2_output | 40.9 | |
| 1B9_hisat2 | 72.6% | |
| 1C10-hisat2_output | 30.3 | |
| 1C10_hisat2 | 71.7% | |
| 1C4-hisat2_output | 36.8 | |
| 1C4_hisat2 | 75.2% | |
| 1D10-hisat2_output | 38.4 | |
| 1D10_hisat2 | 76.8% | |
| 1D3-hisat2_output | 28.2 | |
| 1D3_hisat2 | 73.6% | |
| 1D4-hisat2_output | 43.6 | |
| 1D4_hisat2 | 76.1% | |
| 1D6-hisat2_output | 33.5 | |
| 1D6_hisat2 | 77.5% | |
| 1D8-hisat2_output | 27.1 | |
| 1D8_hisat2 | 69.5% | |
| 1D9-hisat2_output | 38.3 | |
| 1D9_hisat2 | 68.9% | |
| 1E1-hisat2_output | 40.1 | |
| 1E1_hisat2 | 74.3% | |
| 1E3-hisat2_output | 34.4 | |
| 1E3_hisat2 | 77.5% | |
| 1E5-hisat2_output | 33.1 | |
| 1E5_hisat2 | 78.2% | |
| 1E9-hisat2_output | 39.3 | |
| 1E9_hisat2 | 76.8% | |
| 1F11-hisat2_output | 28.0 | |
| 1F11_hisat2 | 71.3% | |
| 1F4-hisat2_output | 32.9 | |
| 1F4_hisat2 | 77.7% | |
| 1F8-hisat2_output | 40.0 | |
| 1F8_hisat2 | 73.8% | |
| 1G5-hisat2_output | 41.8 | |
| 1G5_hisat2 | 76.5% | |
| 1H11-hisat2_output | 32.7 | |
| 1H11_hisat2 | 79.8% | |
| 1H12-hisat2_output | 27.5 | |
| 1H12_hisat2 | 74.2% | |
| 1H6-hisat2_output | 40.0 | |
| 1H6_hisat2 | 73.8% | |
| 1H7-hisat2_output | 31.5 | |
| 1H7_hisat2 | 78.2% | |
| 1H8-hisat2_output | 34.5 | |
| 1H8_hisat2 | 79.1% | |
| 2B2-hisat2_output | 45.3 | |
| 2B2_hisat2 | 74.4% | |
| 2B3-hisat2_output | 32.7 | |
| 2B3_hisat2 | 72.7% | |
| 2C1-hisat2_output | 21.4 | |
| 2C1_hisat2 | 48.5% | |
| 2C2-hisat2_output | 31.8 | |
| 2C2_hisat2 | 75.0% | |
| 2D2-hisat2_output | 39.1 | |
| 2D2_hisat2 | 66.1% | |
| 2E2-hisat2_output | 22.1 | |
| 2E2_hisat2 | 56.9% | |
| 2F1-hisat2_output | 54.0 | |
| 2F1_hisat2 | 72.1% | |
| 2G1-hisat2_output | 25.5 | |
| 2G1_hisat2 | 60.6% |
Samtools
Samtools is a suite of programs for interacting with high-throughput sequencing data.DOI: 10.1093/bioinformatics/btp352.
Samtools Flagstat
This module parses the output from samtools flagstat. All numbers in millions.
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.
