Wiki » History » Version 2
Katie Lennard, 07/13/2018 01:41 PM
| 1 | 1 | Katie Lennard | # Wiki |
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| 2 | # Project resources |
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| 3 | This project will involve single cell RNAseq, which may have additional preprocessing/analysis requirements not currently implemented in our RNAseq pipeline at https://github.com/uct-cbio/RNAseq-pipeline. One major challenge in single cell RNA seq stems from the fact that only a small subset of genes, maybe 1000-2000 are detected (zero-inflated, noisy data). Another challenge is to get cells to cluster by type instead of by other sources of variation such as stage in the cell cycle. See https://www.10xgenomics.com/10x-university/single-cell/ for a screencast introduction. |
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| 5 | Potentially useful resources specific to RNAseq data include: |
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| 6 | * List of tools specifically for single cell RNAseq analysis: http://www.scrna-tools.org/ |
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| 7 | * Possible options for downstream analyses for this list include |
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| 8 | > * Monocle (R/Bioconductor) https://bioconductor.org/packages/release/bioc/html/monocle.html |
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| 9 | > * Seurat (R) https://satijalab.org/seurat/ |
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| 10 | > * Cellranger (mentioned by Walter who sent this support request) - GUI-based? Takes .fastq files as input https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/map/cr-counter |
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| 11 | 2 | Katie Lennard | * RNAtor: Android app. for planning RNAseq experiments e.g. 'How many reads do I need to detect at least 1.5 fold change in transcript expression'? - https://www.biorxiv.org/content/biorxiv/early/2016/12/19/095315.full.pdf |