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Started on 2017-09-05 13:27:37

FastqScreen_Result

FastqScreen Mapping Rates Overview

FastqScreen Mapping Per Sample

Mapping to RefSeq mRNA Per Sample

Virus Check

Settings

settings
Configuration File:
RefSeq mRNA Reference: /srv/GT/reference/RefSeq/mRNA/20150301/Sequence/BOWTIE2Index/transcriptome
FastqScreen Version: 0.11.1
Bowtie2 Version: 2.3.2
Bowtie2 Parameters: -k 10 –trim5 4 –trim3 4 –very-sensitive
Minimum AlignmentScore: -20
TopSpecies: 5

Input Dataset

SessionInfo

## R version 3.4.0 (2017-04-21)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 8 (jessie)
## 
## Matrix products: default
## BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
## LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats4    parallel  stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] htmltools_0.3.6            DT_0.2                    
##  [3] kableExtra_0.2.1           knitr_1.16                
##  [5] rmarkdown_1.5              ShortRead_1.34.0          
##  [7] GenomicAlignments_1.12.1   SummarizedExperiment_1.6.3
##  [9] DelayedArray_0.2.4         matrixStats_0.52.2        
## [11] Biobase_2.36.2             Rsamtools_1.28.0          
## [13] BiocParallel_1.10.1        ezRun_1.0.15              
## [15] GenomicRanges_1.28.3       GenomeInfoDb_1.12.0       
## [17] Biostrings_2.44.0          XVector_0.16.0            
## [19] IRanges_2.10.1             S4Vectors_0.14.1          
## [21] BiocGenerics_0.22.0        data.table_1.10.4         
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_0.12.11            highr_0.6              
##  [3] compiler_3.4.0          RColorBrewer_1.1-2     
##  [5] bitops_1.0-6            tools_3.4.0            
##  [7] zlibbioc_1.22.0         digest_0.6.12          
##  [9] jsonlite_1.4            evaluate_0.10          
## [11] lattice_0.20-35         Matrix_1.2-10          
## [13] yaml_2.1.14             GenomeInfoDbData_0.99.0
## [15] xml2_1.1.1              httr_1.2.1             
## [17] hwriter_1.3.2           stringr_1.2.0          
## [19] htmlwidgets_0.8         rprojroot_1.2          
## [21] grid_3.4.0              R6_2.2.1               
## [23] latticeExtra_0.6-28     magrittr_1.5           
## [25] backports_1.1.0         rvest_0.3.2            
## [27] stringi_1.1.5           RCurl_1.95-4.8