Merge branch 'main' of https://github.com/MMARINeDNA/metabarcoding_QA…

…QC_pipeline

README.md

@@ -47,19 +47,19 @@ cp ./bin/*  ~/Desktop/muri_metabarcoding/scripts
 cp -r ./metadata/* ~/Desktop/muri_metabarcoding/metadata
 ```
 
-## Step 3: Move Raw Fastq's into raw_fastq
+## Step 3: Move Raw Fastq's into raw_fastq and Sample Sheet to metadata
 ---
 Copy your raw fastq's into the raw_fastq directory.  A command that would do this would look like:
 
 ```
-cp /path/to/fastqs/* /path/to/raw_fastqs
+cp /path/to/fastqs/* /path/to/muri_metabarcoding/raw_fastqs
 ```
 Then, copy your Miseq Sample Sheet (which is produced after Illumina sequencing) to the metadata file.
 ```
 cp /path/to/SampleSheetUsed.csv /path/to/muri_metabarcoding/metadata
 ```
 
-## Step 4: Run metabarcoding_wrapper.sh
+## Step 4: Run metabarcoding_wrapper.sh 
 ---
 The metabarcoding wrapper takes 2 inputs:
 * path to your file system (named muri_metabarcoding)