A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2021-02-26, 09:51
based on data in:
/mnt/lustre/agalicina/FUNGI/distiller-nf/stats_collected
General Statistics
Showing 6/6 rows and 6/6 columns.| Sample Name | M read pairs | % unmapped | % single-side mapped | % both-side mapped | % duplicated | % cis |
|---|---|---|---|---|---|---|
| 1441-1.schizo_1441_scaffolds | 69.2 | 12.8% | 45.6% | 41.5% | 4.4% | 64.9% |
| 1441-1.schizo_X44_scaffolds | 71.9 | 22.7% | 56.2% | 21.2% | 2.4% | 66.1% |
| 1441-2.schizo_1441_scaffolds | 80.2 | 13.0% | 46.2% | 40.8% | 5.3% | 64.6% |
| 1441-2.schizo_X44_scaffolds | 83.4 | 23.3% | 56.2% | 20.5% | 2.9% | 66.0% |
| X44-1.schizo_1441_scaffolds | 56.4 | 26.9% | 53.1% | 20.1% | 1.9% | 68.7% |
| X44-1.schizo_X44_scaffolds | 52.0 | 11.5% | 29.7% | 58.8% | 5.1% | 65.6% |
pairtools
pairtools pairtools is a command-line framework for processing sequencing data generated with Chromatin Conformation Capture based experiments: pairtools can handle pairs of short-reads aligned to a reference genome, extract 3C-specific information and perform common tasks, such as sorting, filtering and deduplication.
Pairs alignment status
Number of pairs classified according to their alignment status, including uniquely mapped (UU), unmapped (NN), duplicated (DD), and others.
For further details check pairtools documentation.
Pre-filtered pairs grouped by genomic separations
Distribution of pre-filtered pairs (UU, UR and RU) by genomic separations for
Pre-filtered read pairs might still include artifacts: Short-range cis-pairs are typically enriched in technical artifacts, such as self-circles, dangling-ends, etc. High fraction of trans interactions typically suggests increased noise levels
Frequency of interactions as a function of genomic separation
Frequency of interactions (pre-filtered pairs) as a function of genomic separation, known as "scaling plots", P(s). Click on an individual curve to reveal P(s) for different read pair orientations.
Short-range cis-pairs are typically enriched in technical artifacts. Frequency of interactions for read pairs of different orientations ++,+-,-+ and -- (FF, FR, RF, RR) provide insight into these technical artifacts. Different technical artifacts manifest themselves with only single type of read orientation (dangling-ends - FR, self-circles - RF). Thus enrichment of FR/RF pairs at a given genomic separation can hint at the level of contamination.
Fraction of read pairs by strand orientation
Number of interactions (pre-filtered pairs) reported for every type of read pair orientation. Numbers are reported for different ranges of genomic separation and combined.
Short-range cis-pairs are typically enriched in technical artifacts. Frequency of interactions for read pairs of different orientations ++,+-,-+ and -- (FF, FR, RF, RR) provide insight into these technical artifacts. Different technical artifacts manifest themselves with only single type of read orientation (dangling-ends - FR, self-circles - RF). Thus enrichment of FR/RF pairs at a given genomic separation can hint at the level of contamination.
Pre-filtered pairs grouped by chromosomes
Number of pre-filtered interactions (pairs) within a single chromosome or for a pair of chromosomes.
Numbers of pairs are normalized by the total number of pre-filtered pairs per sample. Number are reported only for chromosomes/pairs that have >1% of pre-filtered pairs. [THERE SEEM TO BE A BUG IN MULTIQC HEATMAP - OBVIOUS WHEN USE HIGHLIGHTING,RENAMING ETC]
