From 481c2c39d614470c34e52bf86a0e6d130ce4007d Mon Sep 17 00:00:00 2001
From: Anton Nekrutenko <anekrut@gmail.com>
Date: Tue, 23 Apr 2024 10:23:27 -0400
Subject: [PATCH] Update project.md

---
 2024/project.md | 38 +++++++++++++++++++++++++++++++++++++-
 1 file changed, 37 insertions(+), 1 deletion(-)

diff --git a/2024/project.md b/2024/project.md
index 3f1a9a4..959bf55 100644
--- a/2024/project.md
+++ b/2024/project.md
@@ -14,7 +14,7 @@ I have subdivided this class into the following groups:
 
 These numbers correspond to colony labels in Fig S3 of the [supplement](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5534434/bin/NIHMS874162-supplement-Supplemental_Methods_And_Figures.pdf).
 
-## Task 1 
+## Task 1: Prep
 (due March 26, 2024 in class)
 
 1. Go to NCBI SRA
@@ -34,3 +34,39 @@ Here:
 **Start point** - point with the number that was assigned to your group (e.g., Point 4 for Manifold4)
 
 Now all numbers were sequenced. So you objective is to find adaptation trajectory which has the data in SRA.
+
+## Task 2: Analysis
+(due May 1st, 2024 by email)
+
+### Assumptions
+
+1. You have a final varinat dataset for your samples (see below for an example)
+2. You have created a mapping between your samples and accession numbers as was [described here](https://github.com/nekrut/BMMB554/blob/master/2024/assessimg_variants.md#establish-the-relationship-between-samples-and-accessions) and downloaded it as a .csv file named `names.csv`.
+
+Example of variant dataset:
+
+```
+Sample	CHROM	POS	REF	ALT	AF	DP	DP4	EFF[*].GENE	EFF[*].CODON	EFF[*].FUNCLASS
+SRR3722117	CP009273	360103	C	T	0.075949	79	30,43,0,6	.	.	NONE
+SRR3722117	CP009273	870516	G	T	0.157895	19	10,6,2,1	yliE	ctG/ctT	SILENT
+SRR3722117	CP009273	1330682	G	T	0.363636	11	4,3,2,2	acnA	Ggt/Tgt	MISSENSE
+SRR3722117	CP009273	1631797	C	A	0.25	16	4,8,2,2	ydfJ	.	NONE
+```
+### What do do
+
+1. Create a copy of this nodebook -> https://colab.research.google.com/drive/1hnoNGQx7MEORWv7KcQAMzpFIsRxvdYVM?usp=sharing
+2. Upload you `names.csv` file into notebook disk
+3. Run your samples through the notebook
+
+#### Group 1 (Sym) 
+
+1. Identify which FIXED mutations are shared within clusters. 
+2. Plot a comparison of these mutations across clusters
+   
+#### Gloups 2 - 4 (Manifold)
+
+1. Identify all fixed mutations that are present in the terminal points but are absent at the start
+2. Trace their trajectroies through the time points from beginning to end
+3. Plot the change in frequencies
+
+