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Old 05-10-2019, 03:24 AM   #2
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,961

You should consider using featureCounts. You may not need a loop. You can feed all SAM files to featureCounts and generate a read count matrix directly.

featureCounts <options> file1.sam file2.sam file3.sam etc.
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