fetalliver dataset doc

sinanugur · Apr 22, 2023 · 6a7222c · 6a7222c
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diff --git a/docs/fetalliver.md b/docs/fetalliver.md
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 Example run on Fetal Liver dataset 
-----------------------------------
+----------------------------------
+Cellsnake can be run directly using the snakemake workflow. We recommend the wrapper but the snakemake workflow give more control in some use cases.
+
+Lets try workflow on Fetal Liver dataset. You can download the dataset here:
+
+
+
+Since this dataset have 6 samples, rather than one MT percentage, make it automatic so that each sample. A minimal run is also enough, we do not want to analyze samples seperately.
+
+```shell
+snakemake -j 10 --config option=minimal percent_mt=auto
+```
+
+Then we can run integration.
+```shell
+snakemake -j 10 --config option=integration
+```
+
+Now it is time to work on the integrated sample. We can run full advanced run on the integrated object which is always generates at the same location.
+```shell
+snakemake -j 10 --config  datafolder=analyses_integrated/seurat/integrated.rds resolution=0.3 route=advanced is_integrated_sample=True --rerun-incomplete
+```
+
+
+
diff --git a/docs/index.rst b/docs/index.rst
@@ -19,5 +19,6 @@ A command line tool for easy and scalable single cell analysis
    installation.md
    quickstart.md
    fetalbrain.md
+   fetalliver.md
    output.md
    options.md