Betacoronavirus-specific alternate splicing
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SciScore for 10.1101/2021.07.02.450920: (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 All these datasets were downloaded from NCBI’s Short Read Archive (SRA) [19]. Short Read Archivesuggested: NoneExcept for the nasal swab (NSPP) dataset [27], all datasets were processed using a snakemake pipeline that performs the following steps: samples are downloaded from the SRA, quality-control is performed using fastp [30], alignment to Genome Reference Consortium Human Build 38 version 91 is done using STAR [31], and isoform quantification carried out by RSEM [32]. RSEMsuggested: (RSEM, RRID:SCR_013027)Reads classified as human using Kraken2 [33] were processed as described in … SciScore for 10.1101/2021.07.02.450920: (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 All these datasets were downloaded from NCBI’s Short Read Archive (SRA) [19]. Short Read Archivesuggested: NoneExcept for the nasal swab (NSPP) dataset [27], all datasets were processed using a snakemake pipeline that performs the following steps: samples are downloaded from the SRA, quality-control is performed using fastp [30], alignment to Genome Reference Consortium Human Build 38 version 91 is done using STAR [31], and isoform quantification carried out by RSEM [32]. RSEMsuggested: (RSEM, RRID:SCR_013027)Reads classified as human using Kraken2 [33] were processed as described in https://github.com/asaravia-butler/COV-IRT/blob/main/RNAseq/Raw_to_Aligned_Data_Pipeline.md and https://github.com/asaravia-butler/COV-IRT/blob/main/RNAseq/RSEM_Counts_Pipeline.md. First, adapters and low-quality data were trimmed with Trimmomatic (v0.39) [34]. Kraken2suggested: NoneTrimmomaticsuggested: (Trimmomatic, RRID:SCR_011848)Kraken2-human classified raw and trimmed read quality were evaluated with FastQC (v0.11.9) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and MultiQC (v1.9) [35] was used to generate MultiQC reports. FastQCsuggested: (FastQC, RRID:SCR_014583)MultiQCsuggested: (MultiQC, RRID:SCR_014982)Homo sapiens STAR and RSEM references were built using STAR (v2.7.3a) [31] and RSEM (v1.3.1) [32], respectively, with Ensembl release 100 human genome version GRCh38 (Homo_sapiens.GRCh38.dna.primary_assembly concatenated with the SARS-CoV-2 Wuhan-Hu-1 SARS-CoV-2 reference genome ASM985889v3, and the following Ensembl gtf annotation file: Homo_sapiens.GRCh38.100.gtf concatenated with Sars_cov_2.ASM985889v3.101.gtf. rRNA-depleted trimmed reads were aligned to the Homo sapiens and SARS-CoV-2 STAR reference with STAR twopassMode (v2.7.3a) [31]. STARsuggested: (STAR, RRID:SCR_004463)Ensemblsuggested: (Ensembl, RRID:SCR_002344)Gene Ontology Analysis: We implemented a version of the Ontologizer [39] analysis code in our Java library phenol (https://github.com/monarch-initiative/phenol). Ontologizersuggested: (Ontologizer, RRID:SCR_005801)Results from OddPub: Thank you for sharing your code.
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.
Results from scite Reference Check: We found no unreliable references.
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