SUSHI Report

Started on 2024-04-26 13:13:07

FastQC_Result

Read Counts

The read counts in each sample.

Fastqc Quality Measures

The summary of FastQC reports.

	Basic Statistics	Per base sequence quality	Per sequence quality scores	Per base sequence content	Per sequence GC content	Per base N content	Sequence Length Distribution	Sequence Duplication Levels	Overrepresented sequences	Adapter Content
NA12878_chr10_R1
NA12878_chr10_R2
NA12889_chr10_R1
NA12889_chr10_R2
NA12890_chr10_R1
NA12890_chr10_R2
NA12891_chr10_R1
NA12891_chr10_R2
NA12892_chr10_R1
NA12892_chr10_R2

Per Base Read Quality

The black and white heatmaps show the average reads quality
over all samples per base. The color scale corresponds to the percentage of reads at each reads quality.

The blue and read heatmaps show the difference between each sample’s reads quality and the average reads quality per base. The red represents a higher percentage of reads over the average, while the blue represents a lower percentage of reads over the average.

Correlation

Correlation between Library concentration measurements and ReadCounts. It’s only shown when “LibConc_qPCR” or “LibConc_100_800bp” columns exit in dataset.

Heatmaps of reads/concentration per cell on the plate

Sequenced reads or concentration per cell, on the plate layout. The current supported plate layout format is “PlateNumber_[A-Z][Integer]”, e.g. “1_A2”. Otherwise, the platelayout is not shown.

The heatmap values are in \(log10\) scale. The colorScale ranges from half of median value to twice of median value.

Input Dataset

SessionInfo

## ezRun tag: c374ec67050e41361e171788c4b5e55b055634c9 
## ezRun github link: https://github.com/uzh/ezRun/tree/c374ec67050e41361e171788c4b5e55b055634c9 
##  
## R version 4.3.2 (2023-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 10 (buster)
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so;  LAPACK version 3.8.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: Europe/Zurich
## tzcode source: system (glibc)
## 
## attached base packages:
##  [1] grid      parallel  stats4    stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] htmltools_0.5.7      DT_0.30              gridExtra_2.3       
##  [4] reshape2_1.4.4       plotly_4.10.3        ezRun_3.18.1        
##  [7] lubridate_1.9.3      forcats_1.0.0        stringr_1.5.1       
## [10] dplyr_1.1.4          purrr_1.0.2          readr_2.1.4         
## [13] tidyr_1.3.0          tibble_3.2.1         ggplot2_3.5.0       
## [16] tidyverse_2.0.0      GenomicRanges_1.54.1 Biostrings_2.70.1   
## [19] GenomeInfoDb_1.38.1  XVector_0.42.0       IRanges_2.36.0      
## [22] S4Vectors_0.40.2     BiocGenerics_0.48.1  data.table_1.14.8   
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.4            xfun_0.41               bslib_0.5.1            
##  [4] htmlwidgets_1.6.2       tzdb_0.4.0              crosstalk_1.2.0        
##  [7] vctrs_0.6.4             tools_4.3.2             bitops_1.0-7           
## [10] generics_0.1.3          fansi_1.0.5             highr_0.10             
## [13] pkgconfig_2.0.3         lifecycle_1.0.4         GenomeInfoDbData_1.2.11
## [16] farver_2.1.1            compiler_4.3.2          munsell_0.5.0          
## [19] sass_0.4.7              RCurl_1.98-1.13         yaml_2.3.7             
## [22] lazyeval_0.2.2          pillar_1.9.0            crayon_1.5.2           
## [25] jquerylib_0.1.4         ellipsis_0.3.2          cachem_1.0.8           
## [28] tidyselect_1.2.0        digest_0.6.33           stringi_1.8.2          
## [31] labeling_0.4.3          fastmap_1.1.1           colorspace_2.1-0       
## [34] cli_3.6.1               magrittr_2.0.3          utf8_1.2.4             
## [37] withr_2.5.2             scales_1.3.0            timechange_0.2.0       
## [40] rmarkdown_2.25          httr_1.4.7              hms_1.1.3              
## [43] evaluate_0.23           knitr_1.45              viridisLite_0.4.2      
## [46] rlang_1.1.3             Rcpp_1.0.11             glue_1.6.2             
## [49] jsonlite_1.8.7          plyr_1.8.9              R6_2.5.1               
## [52] zlibbioc_1.48.0