Update 04_mysterySampleID.md

change year

2023_edition/04_mysterySampleID.md

@@ -8,7 +8,7 @@ Oxford Nanopore sequencers output the raw data in fast5 format. Fast5s contain t
 
 ```bash
 #recall your folder name
-export me=$GROUP_SCRATCH/biochem_minicourse_2022/<your_dir>
+export me=$GROUP_SCRATCH/biochem_minicourse_2023/<your_dir>
 
 #Go to your data folder we created earlier & create subfolders that the fastq files will go in. Change sampleX to your sample number.
 
@@ -17,7 +17,7 @@ mkdir sampleX
 ```
 Copy the data for your sample from the straightlab foler. Change sampleX to your sameple number (ie. sample2). Repeat this for each sample number for your group
 ```
-cp $GROUP_SCRATCH/biochem_minicourse_2022/straightlab/data/samples/sampleX.fastq $me/data/samples
+cp $GROUP_SCRATCH/biochem_minicourse_2023/straightlab/data/samples/sampleX.fastq $me/data/samples
 ```
 
 ## BasicQC
@@ -39,7 +39,7 @@ fastqc $me/data/samples/sampleX.fastq -t 2
 ```
 Transfer the output file to the Downloads folder on your computer. Be sure to change the directory to match your fastqc output.
 ```
-rsync -ah --progress <username>@dtn.sherlock.stanford.edu:/scratch/groups/astraigh/biochem_minicourse_2022/<your_dir>/data/samples/sampleX_fastqc.html ~/Downloads
+rsync -ah --progress <username>@dtn.sherlock.stanford.edu:/scratch/groups/astraigh/biochem_minicourse_2023/<your_dir>/data/samples/sampleX_fastqc.html ~/Downloads
 ```
 Run on your local terminal:
 ```
@@ -68,10 +68,10 @@ head -n 100 sampleX.fasta > sampleX.head.fasta
 
 We have multipe databases installed on sherlock, which correspond to some of those available on ncbi blast online. Here, because we know we what type of samples we are dealing with we have downloaded just a few databases and combined them into one blastdb. The path of this database is  
 ```
-/scratch/groups/astraigh/biochem_minicourse_2022/straightlab/blastdb/combined_db
+/scratch/groups/astraigh/biochem_minicourse_2023/straightlab/blastdb/combined_db
 
 #We can set a variable for this blast database so we don't have to type out the full path eachtime
-export myblastdb=/scratch/groups/astraigh/biochem_minicourse_2022/straightlab/blastdb/combined_db
+export myblastdb=/scratch/groups/astraigh/biochem_minicourse_2023/straightlab/blastdb/combined_db
 
 ```
 
@@ -109,5 +109,5 @@ There are several other output format options that you can use to customize blas
 We can run a simple python script to summarize the blast output by species
 
 ```
-python /scratch/groups/astraigh/biochem_minicourse_2022/straightlab/scripts/summarize_species.py blast/sampleX_sort.output.first50.tsv blast/sampleX_species_summary.tsv
+python /scratch/groups/astraigh/biochem_minicourse_2023/straightlab/scripts/summarize_species.py blast/sampleX_sort.output.first50.tsv blast/sampleX_species_summary.tsv
 ```