Author: Hölzer, Martin; Schoen, Andreas; Wulle, Julia; Müller, Marcel A.; Drosten, Christian; Marz, Manja; Weber, Friedemann
Title: Virus- and Interferon Alpha-Induced Transcriptomes of Cells from the Microbat Myotis daubentonii Document date: 2019_8_10
ID: 0co6m9af_50
Snippet: Prior to mapping, all samples were quality checked with FastQC and quality trimmed with a Q20 threshold and a window size of length 4 using Prinseq (v0.20.3) (Schmieder and Edwards, 2011) . Reads shorter than 15 nt were discarded from the analysis. We used SortMeRNA (v2.1) (Kopylova et al., 2012) to detect and remove ribosomal RNAs, possibly still remaining after the ribosomal depletion step during cDNA library preparation. The quality-controlled.....
Document: Prior to mapping, all samples were quality checked with FastQC and quality trimmed with a Q20 threshold and a window size of length 4 using Prinseq (v0.20.3) (Schmieder and Edwards, 2011) . Reads shorter than 15 nt were discarded from the analysis. We used SortMeRNA (v2.1) (Kopylova et al., 2012) to detect and remove ribosomal RNAs, possibly still remaining after the ribosomal depletion step during cDNA library preparation. The quality-controlled and rRNA-depleted reads were mapped to the concatenated reference genomes of M. lucifugus and RVFV using STAR (v2.5.2) with an adjusted --outFilterScoreMinOverLread and --outFilterMatchNminOverLread of 0.4.
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