Description

Change here to match sample description. I.e:

Breast cancer tumor biopsies from study “XX” 2021.
RNAseq protocol: XX
NovaSeq6000 output, processed by dragen v.3.8.

Report for dragen fastqc; RunID Novaseq_RNA_0012

Directory searched for *fastqc_metrics.csv files:

## [1] "Novaseq_RNA_0012"

Aggregated output saved as “Dragen_FastQC_aggregate_RunID.csv”

1- Read Mean quality; Per-Sequence Quality Scores

Total number of reads. Each average Phred-scale quality value is rounded to the nearest integer.

2- Positional Base Mean Quality; Per-Base Quality Scores

Average Phred-scale quality value of bases with a specific nucleotide at a given location in the read. Locations are listed first and can be either specific positions or ranges. The nucleotide is listed second and can be A, C, G, or T. N or ambiguous bases are assumed to have the system default value, usually QV2.

3- Positional Base Content

Number of bases of each specific nucleotide at given locations in the read. Locations are given first and can be either specific positions or ranges. The nucleotide is listed second and can be A, C, G, T, N.

Per-Position Sequence Content heatmap and Per-Position N Content

4- Read length

Total number of reads with each observed length.

5- Read GC Content; Per-Sequence GC Content

Total number of reads with each GC content percentile between 0% and 100%.

6- Read GC Content Quality; Average mean quality for reads by GC%

Average Phred-scale read mean quality for reads with each GC content percentile between 0% and 100%.

7- Sequence Positions; Cumulative Adapter Content

Number of times an adapter or other kmer sequence is found, starting at a given position in the input reads. Sequences are listed first in the metric description in quotes. Locations are listed second and can be either specific positions or ranges.

From the Illumina Dragen manual:
“DRAGEN contains a novel lossless soft-trimming mode. In soft-trimming mode, reads are mapped as though they had been trimmed, but no bases are removed. The intention of soft trimming is to suppress systematic mismapping of reads containing trimmable artifacts, such as Poly-G artifacts, from getting mapped to reference G homopolymers or adapter sequences getting mapped to matching reference loci, without actually losing the trimmed bases in aligned output.”

8- Positional Quality

Phred-scale quality value for bases at a given location and a given quantile of the distribution. Locations are listed first and can be either specific positions or ranges. Quantiles are listed second and can be any whole integer 0–100.

This plot represent the same type of plot as the Box and Whisker plot generated by fastQC. The major difference is that here we plot all values from fastqc output and not just min, max and the interquartile range. For samples with low phred score, the plot will become darker. The brighter the plot, the better the overall score.

sessionInfo()
## R version 4.1.2 (2021-11-01)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur 10.16
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] plotly_4.10.0   forcats_0.5.1   stringr_1.4.0   dplyr_1.0.8    
##  [5] purrr_0.3.4     readr_2.1.2     tidyr_1.2.0     tibble_3.1.6   
##  [9] ggplot2_3.3.5   tidyverse_1.3.1
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.8        lubridate_1.8.0   assertthat_0.2.1  digest_0.6.29    
##  [5] utf8_1.2.2        R6_2.5.1          cellranger_1.1.0  backports_1.4.1  
##  [9] reprex_2.0.1      evaluate_0.14     highr_0.9         httr_1.4.2       
## [13] pillar_1.7.0      rlang_1.0.1       lazyeval_0.2.2    readxl_1.3.1     
## [17] rstudioapi_0.13   data.table_1.14.2 jquerylib_0.1.4   rmarkdown_2.11   
## [21] labeling_0.4.2    htmlwidgets_1.5.4 bit_4.0.4         munsell_0.5.0    
## [25] broom_0.7.12      compiler_4.1.2    modelr_0.1.8      xfun_0.29        
## [29] pkgconfig_2.0.3   htmltools_0.5.2   tidyselect_1.1.1  fansi_1.0.2      
## [33] viridisLite_0.4.0 crayon_1.4.2      tzdb_0.2.0        dbplyr_2.1.1     
## [37] withr_2.4.3       grid_4.1.2        jsonlite_1.7.3    gtable_0.3.0     
## [41] lifecycle_1.0.1   DBI_1.1.2         magrittr_2.0.2    scales_1.1.1     
## [45] cli_3.1.1         stringi_1.7.6     vroom_1.5.7       farver_2.1.0     
## [49] fs_1.5.2          xml2_1.3.3        bslib_0.3.1       ellipsis_0.3.2   
## [53] generics_0.1.2    vctrs_0.3.8       tools_4.1.2       bit64_4.0.5      
## [57] glue_1.6.1        crosstalk_1.2.0   hms_1.1.1         parallel_4.1.2   
## [61] fastmap_1.1.0     yaml_2.2.2        colorspace_2.0-2  rvest_1.0.2      
## [65] knitr_1.37        haven_2.4.3       sass_0.4.0