This step removes technical sequences such as indexes using in Illumina sequencing as well as removing reads of insufficient quality.Įstablish RNA-Seq Sample Set. Trim RNA-Seq reads with Trimmomatic for each PairedEndLibrary. These are based off of RefSeq accession numbers NC_003197.2 and NC_003277.2 respectively. typhimurium LT2 genome and PSLT plasmids).
Upload a suitable, annotated reference genome serving as the basis for RNA-Seq alignment ( S. Sequencing results are the product of HiSeq4000 sequencing using 100PE runs (see Methods). Process Overview ¶īefore the narrative begins, upload RNA-Seq datasets to KBase as PairedEndLibrary Objects. We began from pre-loaded RNA-Seq reads (PairedEndLibrary objects) and output datasets available in Supplementary Datasets 5 and 6 ( doi.org/10.6084/m9.figshare.12185031). In this narrative, we processed RNA-Seq reads into differential expression analysis datasets. The goal of this experiment was to identify shared transcription-level difference between phage cross-resistant mutants, ∆trkH, ∆sapB, ∆rpoN, ∆himA relative to wild-type S. This KBase narrative contains RNA-Seq data processing for Adler et al., "Systematic Discovery of Salmonella Phage-Host Interactions via High-Throughput Genome-Wide Screens", 2020. Adler, Crystal Zhong, Hualan Liu, Elizabeth Kutter, Adam M. Supplemental RNA-Seq Processing Notebook for: ¶ Systematic Discovery of Salmonella Phage-Host Interactions via High-Throughput Genome-Wide Screens ¶ Benjamin A.
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