Evidence for host-dependent RNA editing in the transcriptome of SARS-CoV-2

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1. Version published to 10.1126/sciadv.abb5813

   Jun 17, 2020
2. 

   ScreenIT

   Jun 4, 2020

   SciScore for 10.1101/2020.03.02.973255: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   We used TRIMMOMATIC ( 59 ) to trim the reads of those samples to 100 bp , with the following command line: trimmomatic SE SRR* . fastq SRR* . trimmed.fastq CROP:100 We aligned the FASTQ files using Burrows-Wheeler Aligner ( BWA ) ( 60 ) using the official sequence of SARS-CoV-2 ( NC_045512 . 2 ) as reference genome.	TRIMMOMATIC suggested: (Trimmomatic, SCR_011848)
   | samtools sort –O BAM -o SRR*_ . bam The aligned bams have been analysed with QUALIMAP ( 62) .	samtools suggested: (SAMTOOLS, S…

   SciScore for 10.1101/2020.03.02.973255: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   We used TRIMMOMATIC ( 59 ) to trim the reads of those samples to 100 bp , with the following command line: trimmomatic SE SRR* . fastq SRR* . trimmed.fastq CROP:100 We aligned the FASTQ files using Burrows-Wheeler Aligner ( BWA ) ( 60 ) using the official sequence of SARS-CoV-2 ( NC_045512 . 2 ) as reference genome.	TRIMMOMATIC suggested: (Trimmomatic, SCR_011848)
   | samtools sort –O BAM -o SRR*_ . bam The aligned bams have been analysed with QUALIMAP ( 62) .	samtools suggested: (SAMTOOLS, SCR_002105)
   Due to a high error rate reported by QUALIMAP , samples SRR11059943 and SRR10971381 have been removed from the analysis .	QUALIMAP suggested: (QualiMap, SCR_001209)
   To avoid potential artifacts due to strand bias , we used the AS_StrandOddsRatio parameter calculated following GATK guidelines ( ( https://gatk.broadinstitute.org/hc/en-us/articles/360040507111-AS- StrandOddsRatio) , and any mutation with a AS_StrandOddsRatio > 4 has been removed from the dataset.	GATK suggested: (GATK, SCR_001876)
   bam Mutations common to the datasets generated by Reditools 2 and JACUSA were considered ( n = 910 , Fig .	Reditools suggested: (REDItools, SCR_012133)
   Data manipulation R packages ( Biostrings , rsamtools , ggseqlogo ggplot2 , splitstackshape ) and custom Perl scripts were used to handle the data .	ggplot2 suggested: (ggplot2, SCR_014601)
   SARS-CoV-2 , SARS and MERS genomic data were prepared for the Logi alignment using the GenomicRanges R package ( 63)	GenomicRanges suggested: (GenomicRanges, SCR_000025)
   Consensus sequences of SARS and MERS genomes were built using the “cons” tool from the EMBOSS suite (http://bioinfo.nhri.org.tw/gui/) with default settings.	EMBOSS suggested: (EMBOSS, SCR_008493)
   SARS-CoV-2 genomic sequences were downloaded from GISAID (https://www.gisaid.org/) and aligned with MUSCLE (64).	MUSCLE suggested: (MUSCLE, SCR_011812)

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   SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.

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3. 

   Version published to 10.1101/2020.03.02.973255 on bioRxiv

   Mar 3, 2020