From b02a5c2f81746b11e6877c564a6e6b4a18c19ee8 Mon Sep 17 00:00:00 2001
From: Cassidy Johnson <114778057+cassidy-a-johnson@users.noreply.github.com>
Date: Thu, 21 Sep 2023 23:15:02 -0400
Subject: [PATCH] Update kreeq.md

---
 docs/kreeq.md | 44 ++++++++++++++++++++++++++++++++++----------
 1 file changed, 34 insertions(+), 10 deletions(-)

diff --git a/docs/kreeq.md b/docs/kreeq.md
index f27b375..79126ce 100644
--- a/docs/kreeq.md
+++ b/docs/kreeq.md
@@ -1,26 +1,32 @@
-Let's get some test files first:
-```
-mv testFiles-kreeq/* .
-```
+The standard notation for using kreeq is as follows:
 ```
 kreeq validate -f input.[fasta|fastq][.gz] -r reads1.fastq[.gz] reads2.fastq[.gz] [...] [-k 21]
 ```
 
-It accepts multiple read files as input, separated by space. To check out all options and flags use: 
-
-`kreeq -h`
+It accepts multiple read files as input, separated by space. The two modes we will be using today are `validate` and `union`.
+To check out all options and flags use: 
+```
+kreeq -h
+kreeq validate -h
+kreeq union -h
+```
 
-You can test some typical usage with the files in the `testFiles` folder, e.g.:
+Let's get some test files first:
+```
+mv gfastar/docs/testFiles-kreeq/* .
+```
 
+We will test some typical usage with the files moved from the `testFiles` folder, e.g.:
 ```
 kreeq validate -f random1.fasta -r random1.fastq
+kreeq validate -f random2.fasta -r random1.fastq random2.fastq
 ```
 
 Importantly, the kreeq database can only be computed once on the read set, and reused for multiple analyses to save runtime:
 
 ```
-kreeq validate -r random1.fastq -o db.kreeq
-kreeq validate -f random1.fasta -d db.kreeq
+kreeq validate -r random1.fastq -o random1.kreeq
+kreeq validate -f random1.fasta -d random1.kreeq
 ```
 
 Similarly, kreeq databases can be generated separately for multiple inputs and combined, with increased performance in HPC environments:
@@ -32,3 +38,21 @@ kreeq validate -r random2.fastq -o random2.kreeq
 kreeq union -d random1.kreeq random2.kreeq -o union.kreeq
 kreeq validate -f random1.fasta -d union.kreeq
 ```
+
+Now working with real sequencing data:
+
+Let's start by running `gfastats` to get a sense of what we are evaluating.
+```
+gfastats input.fa
+```
+
+Now we are ready to run kreeq:
+```
+kreeq validate -r filtered.fastq -o filtered.kreeq
+kreeq validate -r filtered2.fastq -o filtered2.kreeq
+
+kreeq union -d filtered.kreeq filtered2.kreeq -o filtered_union.kreeq
+
+kreeq validate -f input.fa -d filtered_union.kreeq
+```
+```