From 0fc18547d6db8cf373e8da43a7dea38e89c93869 Mon Sep 17 00:00:00 2001 From: "Adri K. Grow" <42044618+adriannagrow@users.noreply.github.com> Date: Fri, 22 Aug 2025 13:16:37 -0400 Subject: [PATCH] Update ReadMapping.py --- Utilities/for_taxonomy/ReadMapping.py | 1 + 1 file changed, 1 insertion(+) diff --git a/Utilities/for_taxonomy/ReadMapping.py b/Utilities/for_taxonomy/ReadMapping.py index 09bf6bf..c647385 100644 --- a/Utilities/for_taxonomy/ReadMapping.py +++ b/Utilities/for_taxonomy/ReadMapping.py @@ -32,6 +32,7 @@ for x in folder: #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.remove("sample.sam") 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")