Update README.md

README.md

@@ -206,7 +206,7 @@ bash workflow/scripts/nanoplot.sh -t 1 -j 1 -o .test/stats_out -i .test/test_dat
 ```
 This visualisation will display the read characteristics for each sample, facilitating the configuration of ONT-AmpSeq. An easy way to assess the amplicon length and quality is through the provided plot `LengthvsQualityScatterPlot_dot.png`.
 <figure id="figref-nanoplot">
-  <img src=".test/stats_out/stats/sample1/LengthvsQualityScatterPlot_dot.png">
+  <img src="example_figures/LengthvsQualityScatterPlot_dot.png">
   <figcaption>
   <strong>Figure 1:</strong> Dot plot of the test data. Visualising read length on the x-axis and Q-score on the y-axis. This example reveals reads characteristics for one distinct amplicon for the 16S rRNA V1-8. 
   </figcaption>
@@ -445,4 +445,4 @@ All information regarding configurations of the pipeline for a given run, is cap
 The pipeline outputs OTU-tables with 97% and 99% identity ready for [Ampvis2](https://kasperskytte.github.io/ampvis2/index.html) and files ready to load into [phyloseq](https://github.com/joey711/phyloseq), all located in `~/example_case/ONT-AmpSeq-main/reslts/final` in a sub-folder corresponding to their %identity, more information on outputs can be found [here](#output-files). Explanation of all output file can be found [here](#output-files). Furthermore, initial plots are made using Ampvis2 and the metadata sheet:
 <figure id="figref-nanoplot">
   <img src="example_figures/Heatmap_99_sintax.png">
-</figure>
+</figure>