Proteo-Genomic Analysis of SARS-CoV-2: A Clinical Landscape of Single-Nucleotide Polymorphisms, COVID-19 Proteome, and Host Responses
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SciScore for 10.1101/2020.11.27.20237032: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Samples were collected only after the approved consent of the patients who were informed about the study.
IACUC: The study was conducted after approval of the institutional human ethics committee, IISc (19-01092020).Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Mutation analysis: Initially, the quality of the reads was checked using FastQC v0.11.9.7 Further, the sequencing adapters clipped at 5’ and 3’ end of reads were trimmed using Cutadapt v2.9.8 The adapter trimmed pair-end reads were then aligned to the Wuhan reference … SciScore for 10.1101/2020.11.27.20237032: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Samples were collected only after the approved consent of the patients who were informed about the study.
IACUC: The study was conducted after approval of the institutional human ethics committee, IISc (19-01092020).Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Mutation analysis: Initially, the quality of the reads was checked using FastQC v0.11.9.7 Further, the sequencing adapters clipped at 5’ and 3’ end of reads were trimmed using Cutadapt v2.9.8 The adapter trimmed pair-end reads were then aligned to the Wuhan reference genome (Accession No. NC_045512.2) downloaded from NCBI. FastQCsuggested: (FastQC, RRID:SCR_014583)Cutadaptsuggested: (cutadapt, RRID:SCR_011841)9 The fast and accurate read alignment was achieved by using BWA v. BWAsuggested: (BWA, RRID:SCR_010910)10 The aligned reads were sorted, removed soft-clippings and then variant calling was performed using GATK variant caller. GATKsuggested: (GATK, RRID:SCR_001876)11 The reported variants were then annotated to study their effects in proteins and genes using SNPEff tool. SNPEffsuggested: (SnpEff, RRID:SCR_005191)Evolutionary analyses were conducted in MEGA X. MEGAsuggested: (Mega BLAST, RRID:SCR_011920)The raw data were analyzed using MaxQuant software (v1.6.2.10) and processed through the MS excel sheet. MaxQuantsuggested: (MaxQuant, RRID:SCR_014485)The database analysis was performed against SARS-CoV-2 proteome and Homo sapiens proteome in the UniProt database (Proteome ID-UP000005640). UniProtsuggested: (UniProtKB, RRID:SCR_004426)Statistical significance of the genes involved in positive samples was analyzed using the R package, clusterProfiler. clusterProfilersuggested: (clusterProfiler, RRID:SCR_016884)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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