diff --git a/Utilities/for_taxonomy/readmapping.py b/Utilities/for_taxonomy/readmapping.py
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+#python week 6
+#map a group of trimmed reads to a reference
+#IMPORTANT: Please read commented-out (grey) notes. They will tell you where you need to edit the script.
+
+import os
+from Bio import SeqIO
+
+#this first command builds your reference with Hisat.
+#If you've already done this, DON'T run this command! Instead, comment it out (use a # in front of it).
+#It will output several files. Don't worry about them, Hisat will know what to do.
+os.system("hisat2-build NEW_Foram_only_053023.fasta Foram_Index") #change to your reference.fasta and rename the index
+
+folder = os.listdir("TrimmedReads") #Insert the name of the folder which has your trimmed reads inside the quotes
+folder.sort() #This sorts the folder so that all the LKHs are in order.
+
+for x in folder:
+	if "LKH" in x and "FPE" in x: #assigning a variable to forward reads. Make sure you have both forward and reverse reads for each cell!
+		FPE = x
+	if "LKH" in x and "RPE" in x: #assigning a variable to reverse reads.
+		RPE = x
+
+		if(FPE[:7] == RPE[:7]): 
+			#The next few lines are several Hisat commands that will create new files.
+			#EDIT the name of the index and the name of the trimmed reads folder in the first command below
+			os.system("hisat2 -x Foram_Index -1 TrimmedReads/" +FPE+ " -2 TrimmedReads/" +RPE+ " -S sample.sam") 
+			os.system("samtools view -bS sample.sam > sample.bam")
+			os.system("samtools fixmate -O bam sample.bam  fixmate_sample.bam")
+			os.system("samtools sort -O bam -o sorted_sample.bam fixmate_sample.bam")
+			os.system("sambamba markdup -r sorted_sample.bam sorted_sample.dedup.bam")
+			os.system("samtools view -h -b -q 40 sorted_sample.dedup.bam > sorted_sample.q40.bam")
+			os.system("samtools view -h -b -q 20 sorted_sample.dedup.bam > sorted_sample.q20.bam")
+			os.system("samtools view -h -F 4 -b sorted_sample.dedup.bam > defaultparameters_sample.bam")
+
+			if not os.path.isdir(x[:7]):
+				os.mkdir(x[0:7]) #making folders with the names of the LKHs
+				
+			for file in os.listdir('.'): #These lines move the sam/bam files that Hisat creates into the new LKH folders.
+				if(file.endswith('.sam') or file.endswith('.bam')):
+					os.rename(file,x[:7] + '/' + file)
+				
+print("~~~~~~~~~~~:>~") #When the snake appears, your script has run!
+		
+	
+