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3 Normalization
robertprior-fixstars edited this page Sep 23, 2019
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The normalization stage will create symlinks with the same name to all image files created in the previous colour correction stage. For each round a _summedNorm image will be created which is the quantile normalization applied to the input channels. It is important to note that the normalization supports only exactly 4 color channels.
- 1 Setup Cluster
- 2 Color Correction
- 3 Normalization
- 4 Registration
- 5 Puncta Extraction
- 6 Base Calling
- Performance Profile
- Example Batching
- Summary Reporting (link to page) / Analysis (link to page) All of above would be bullet points but thought each folder with useful scripts in the repository would have its own page with example usages and descriptions for the files under the given directory. Unsure on this as haven't used anything under these directories directly myself (i.e not through runPipeline) apart from tests/perf-profile/summarize-stat-logs.sh. Should any of these have a separate page? Note have not made pages for this yet as not sure how many should be made or if this break down makes sense.
- Troubleshooting