Selected article for: "gene level and RNA seq"
Author: Hazel Stewart; Katherine Brown; Adam M. Dinan; Nerea Irigoyen; Eric J. Snijder; Andrew E. Firth
Title: The transcriptional and translational landscape of equine torovirus
  • Document date: 2018_4_7
    • ID: mozfm5ds_77
    Snippet: Differential gene expression analysis. For analysis of host differential expression 660 between non-drug treated infected and mock-infected cells, all reads which did not 661 map to rRNA or vRNA were mapped to the EquCab2.0 reference genome and 662 annotations (Ensembl release 89) using STAR (57) with a maximum of two 663 mismatches and removal of non-canonical, non-annotated splice junctions. Read 664 counts were generated using HTSeq 0.8.0 (63).....
    Document: Differential gene expression analysis. For analysis of host differential expression 660 between non-drug treated infected and mock-infected cells, all reads which did not 661 map to rRNA or vRNA were mapped to the EquCab2.0 reference genome and 662 annotations (Ensembl release 89) using STAR (57) with a maximum of two 663 mismatches and removal of non-canonical, non-annotated splice junctions. Read 664 counts were generated using HTSeq 0.8.0 (63). For differential transcription analysis, 665 gene level counts were generated across the Ensembl release 89 EquCab2.0 gtf file, 666 filtered to include only protein-coding genes. For differential translation efficiency 667 analysis only coding regions (CDS) were considered: both RNA-seq and Ribo-seq 668 counts were generated at CDS level using intersection-strict mode, based on the 669 same annotation set. Multimapping reads were excluded from both analyses. 670

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