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| 2019 | Shiny-Seq - https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-019-4471-1 |
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| | https://github.com/nf-core/rnaseq |
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| | NGS-pipe - https://github.com/cbg-ethz/NGS-pipe/wiki |
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## Metrics for comparing pipelines for RNA-seq analysis
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* Input
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* size of the input that needs to be provided
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* type: Accessions - repositories / Fastq files
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* automated inferences: type of sample preparation, adaptors
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* Output
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* sample quality metrics
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* complexity
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* mapping rate
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* duplication level
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* saturation level
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* RNA integrity
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* bam files
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* quantification
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* gene level
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* isoform level
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* annotation categories
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* proportion structural RNAs
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* includes multi-mappers
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* inference
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* novel isoforms: splicing/polyadenylation
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* SNPs/mutations
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* Number/type of supported platforms
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* Desktop application/needs cluster |