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Update ReadMapping.py

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Adri K. Grow 2025-08-22 13:16:37 -04:00 committed by GitHub
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commit 0fc18547d6
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Utilities/for_taxonomy/ReadMapping.py
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@ -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")