Add tapestri insight and tapestri pipeline final

docs/Tools/Sequencing_tools/singleCell/Tapestri_insight.md

@@ -1,26 +1,33 @@
 # Tapestri insights
 
-!!! note annotate ""
-    Tapestri insights is a software available for Windows and MacOS that allows DNA analysis of single cell data.
+!!! warning "Compatibiliy"
+    The software is **NOT** available for Linux, you need a **Windows** machine or a VM running windows on your Linux machine in order to use it.
 
-## Download
-It is downloadable from the [personal user portal](https://portal.missionbio.com/). 
+    Don't panic! This software is not a mandatory step to analyse the data. Indeed, one can produce the same analysis by using [Mosaic package](Mosaic.md)
+
+## Installation
+
+Download and installation guide is available [here](https://support.missionbio.com/hc/en-us/articles/360058471313-FAQ-How-do-I-download-Tapestri-Insights-v2-2-).
 
 ## Usage
-Tapestri insight has a GUI and does not require command line nor programming skills to run it. 
 
-The file type supported are `.loom` files, that can be found in the list of ouput file from the Tapestri pipeline summary page of the analysis, in the user private page.
+Tapestri insight has a GUI and does not require command line nor programming skills to use it.
 
+The file type supported are `.loom` files, that can be found in the list of ouput file from the [Tapestri pipeline](../Tapestri_pipeline/#3-output) summary page of the analysis, in the user private area.
+
+An optional input could be a whitelist file with known chromosomal locations with pathogenic variants that, even if they do not pass the built-in quality filters, they are still carried on for the analysis.
 
 ## Additional resources
+
 MissionBio provided a personal training course, the video lesson on Tapestri Insights can be found here:
-```
-/workspace/projects/scell_tall/LOPEBIG_44_analysis/mosaic/Video_Trainings/MissionBio-2-TapestriInsight.mp4
-```
+
+    /workspace/projects/scell_tall/LOPEBIG_44_analysis/mosaic/Video_Trainings/MissionBio-2-TapestriInsight.mp4
 
 ## Links
+
 - [Tapestri Insights Demo](https://support.missionbio.com/hc/en-us/articles/360045421074-Tapestri-Insights-Demo)
 - [Tapestri Insights: Visualize Clones](https://support.missionbio.com/hc/en-us/articles/360045157814-Tapestri-Insights-Visualize-clones)
 
 ## Reference
-- Federica Brando
+
+- Federica Brando

docs/Tools/Sequencing_tools/singleCell/Tapestri_pipeline.md

@@ -26,7 +26,7 @@ There are three different options that requires different files:
 - **Reference Genome**. Custom reference file must be in `.fa.zip` format. As of now, there are h19 and mouse reference genomes on Tapestri portal.
 - **Panels**. Both DNA and Protein can be either customed or taken from their [Designer catalog](https://designer.missionbio.com/catalog-panels). Custom Panels files must be in `zip` format.
 - **FASTQ files**. They must be in `.fastq`, `.fastq.gz`, `.fq` or `.fq.gz` format. The number of files must be even.
-- **.h5 files** . Tapestri Pipeline output file of one run. *i.e.* If we have multiple runs of the sample patients but with different stage of the disease we can merge the runs to produce an .h5 file with
+- **.h5 files** . Tapestri Pipeline output file of one run. *i.e.* If we have multiple runs of the sample patients but with different stage of the disease we can merge the runs to produce an .h5 file with both samples.
 
 ### Output