diff --git a/Utilities/for_taxonomy/ReadMapping.py b/Utilities/for_taxonomy/ReadMapping.py
index eeba929..09bf6bf 100644
--- a/Utilities/for_taxonomy/ReadMapping.py
+++ b/Utilities/for_taxonomy/ReadMapping.py
@@ -1,34 +1,35 @@
 '''
 #Author, date: ?
-#Uploaded: updated by Adri Grow, 2024
-#Intent: map a group of trimmed reads to a reference. 
+#Uploaded: updated by Adri Grow, Aug 2025
+#Intent: map a group of trimmed reads to a reference 
 #Dependencies: Python3, hisat2, samtools, sambamba
-#EDIT LINES: 18 & 32
-#Inputs: Folder named 'TrimmedReads' containing all the trimmed reads.
-#Outputs: Folders with the names of the LKHs containing the sam/bam files.
+#EDIT LINES: 18 & 33
+#Inputs: Folder named 'TrimmedReads' containing all the trimmed reads
+#Outputs: Folders with the names of the LKHs containing the sam/bam files
 #Example: python ReadMapping.py
 '''
 
 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 Foram_reference.fasta Foram_Index") #change to your reference.fasta and rename the index
+#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 Foram_reference.fasta Foram_Index") #change to your reference.fasta and (optionally) 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.
+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.
+		sample_id = FPE.split("_FPE")[0]
+	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
+		if FPE.split("_FPE")[0] == RPE.split("_RPE")[0]: # Match sample IDs dynamically 
+			#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 (line 33) if necessary
 			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")
@@ -38,12 +39,12 @@ for x in folder:
 			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
+			if not os.path.isdir(sample_id):
+				os.mkdir(sample_id) #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)
+					os.rename(file, f"{sample_id}/{file}")
 				
 print("~~~~~~~~~~~:>~") #When the snake appears in terminal, your script has finished running!