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xin-huang · May 30, 2024 · 330e5b9 · 330e5b9
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diff --git a/docs/userguide/cache.md b/docs/userguide/cache.md
@@ -33,7 +33,7 @@ Users can use the `--gamma-bounds` option to choose the range of the distributio
 
 The output files [1KG.YRI.CEU.20.split_mig_sel_single_gamma.spectra.bpkl](https://github.com/xin-huang/dadi-cli/blob/revision/examples/results/caches/1KG.YRI.CEU.20.split_mig_sel_single_gamma.spectra.bpkl) and [1KG.YRI.CEU.20.split_mig_sel.spectra.bpkl](https://github.com/xin-huang/dadi-cli/blob/revision/examples/results/caches/1KG.YRI.CEU.20.split_mig_sel.spectra.bpkl) are binary files generated by the Python [pickle](https://docs.python.org/3/library/pickle.html) module. **Note: Since the pickle module can be insecure, only use cache files from trusted sources**.
 
-## Settings
+## Arguments
 
 | Argument | Description |
 | - | - |

diff --git a/docs/userguide/demog.md b/docs/userguide/demog.md
@@ -117,7 +117,7 @@ Because there is randomness built into `dadi-cli` for where the starting paramet
 
 Finally, the grid sizes may also affect the inference. If `n` is the maximum of the sample sizes, then the default grid sizes are `(int(n*1.1)+2, int(n*1.2)+4, int(n*1.3)+6)`.
 
-## Settings
+## Arguments
 
 | Argument | Description |
 | - | - |

diff --git a/docs/userguide/dfe.md b/docs/userguide/dfe.md
@@ -115,7 +115,7 @@ Similar to the best fit parameters in `./examples/results/demog/1KG.YRI.CEU.spli
 |------------|------|-------|-----|-----|-------------------|
 | -1389      | 5.51 | 7.65  | 0   | 0   | 0.017             |
 
-## Settings
+## Arguments
 
 | Argument | Description |
 | - | - |

diff --git a/docs/userguide/fs.md b/docs/userguide/fs.md
@@ -53,7 +53,7 @@ An example for a folded allele frequency spectrum from one population is below.
 1 0 0 1 1
 ```
 
-## Settings
+## Arguments
 
 | Argument | Description |
 | - | - |

diff --git a/docs/userguide/stat.md b/docs/userguide/stat.md
@@ -2,14 +2,16 @@
 
 To perform uncertainty analysis, `dadi` offers [an approach](https://dadi.readthedocs.io/en/latest/user-guide/uncertainty-analysis/) using the Godambe Information Matrix (GIM). To utilize this method, users should begin by using the `GenerateFs` subcommand to generate bootstrapped data from VCF files.
 
-In this example we generate 20 bootstraps to save on time, but we recommend users do 100. `--chunk-size` is the max length of chunks the chromosomes will be broken up into and used to randomly draw from with replacement to make our bootstrapped chromosomes.
+In this example, we generate `20` bootstraps using the `--bootstrap` argument to save time, though we recommend users perform `100` bootstraps for more robust results. The `--chunk-size` argument specifies the maximum length of the chromosome chunks, which are then randomly drawn with replacement to create the bootstrapped chromosomes. The `--output` argument sets the prefix for the output files and the directory where the allele frequency spectra from the bootstrapped chromosomes will be stored.
 
 ```
 dadi-cli GenerateFs --vcf examples/data/1KG.YRI.CEU.syn.vcf.gz --pop-info examples/data/1KG.YRI.CEU.popfile.txt --pop-ids YRI CEU --projections 20 20 --polarized --bootstrap 20 --chunk-size 1000000 --output examples/results/fs/bootstrapping_syn/1KG.YRI.CEU.20.syn
 
 dadi-cli GenerateFs --vcf examples/data/1KG.YRI.CEU.non.vcf.gz --pop-info examples/data/1KG.YRI.CEU.popfile.txt --pop-ids YRI CEU --projections 20 20 --polarized --bootstrap 20 --chunk-size 1000000 --output examples/results/fs/bootstrapping_non/1KG.YRI.CEU.20.non
 ```
 
+The output files from the above commands can be found in the `bootstrapping_syn` directory for synonymous SNPs and the `bootstrapping_non` directory for non-synonymous SNPs [here](https://github.com/xin-huang/dadi-cli/tree/revision/examples/results/fs). 
+
 To estimate the confidence intervals for the demographic parameters, users can use
 
 ```