ATACseq-mapping-report
A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2020-12-01, 02:57
based on data in:
/share/workshop/epigenetics_workshop/msettles/atacseq_example/02-BWA
General Statistics
Showing 7/7 rows and 7/9 columns.| Sample Name | M Reads Mapped | Error rate | M Non-Primary | M Reads Mapped | % Mapped | % Proper Pairs | M Total seqs |
|---|---|---|---|---|---|---|---|
| JLAC003A_bwa | 25.3 | 0.25% | 0.0 | 25.3 | 99.7% | 97.8% | 25.4 |
| JLAC003B_bwa | 41.7 | 0.23% | 0.0 | 41.7 | 99.4% | 97.6% | 42.0 |
| JLAC003C_bwa | 34.2 | 0.20% | 0.0 | 34.2 | 99.8% | 97.9% | 34.2 |
| JLAC004D_bwa | 45.0 | 0.19% | 0.0 | 45.0 | 99.7% | 97.6% | 45.1 |
| JLAC004E_bwa | 39.8 | 0.18% | 0.0 | 39.8 | 99.8% | 97.3% | 39.9 |
| JLAC004F_bwa | 44.5 | 0.17% | 0.0 | 44.5 | 99.9% | 96.9% | 44.5 |
| bwa | 0.0 | 0.00% | 0.0 | 0.0 | 0.0 |
Samtools
Samtools is a suite of programs for interacting with high-throughput sequencing data.
Percent Mapped
Alignment metrics from samtools stats; mapped vs. unmapped reads.
For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.
Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).
Alignment metrics
This module parses the output from samtools stats. All numbers in millions.
Samtools Flagstat
This module parses the output from samtools flagstat. All numbers in millions.
XY counts
Mapped reads per contig
The samtools idxstats tool counts the number of mapped reads per chromosome / contig. Chromosomes with < 0.1% of the total aligned reads are omitted from this plot.
