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In Vivo RNA: RNA Interactions Using the SCRAP Bioinformatics Pipeline

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Peak Calling and Annotation in SCRAP for Small Noncoding RNA: Target RNA Interaction Studies (Video) | JoVE

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Biologie

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Journal JoVE Biologie

Peak Calling and Annotation in SCRAP for Small Noncoding RNA: Target RNA Interaction Studies

Peak Calling and Annotation in SCRAP for Small Noncoding RNA: Target RNA Interaction Studies (Video) | JoVE

In Vivo RNA: RNA Interactions Using the SCRAP Bioinformatics Pipeline

DOI:

10.3791/200890-v

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02:13 min

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December 01, 2023

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Sreenivas Eadara, Xinbei Li, Emily A. Eiss, Mollie K. Meffert²

¹Department of Biological Chemistry,Johns Hopkins University School of Medicine, ²Solomon H. Snyder Department of Neuroscience,Johns Hopkins University School of Medicine

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Peak_calling_directory=/path/to/sample/folders Adapter_file=/path/to/adapter.fasta Min_reads=10 Min_samples=2 Require_same_family=True Reference_dir=/path/to/reference/directory Mirbase_abbr=hsa Genome_abbr=hg38 Peak_file=/path/to/resulting/peaks.bed Bam_file=/path/to/merged.bam Sorted_bam=/path/to/sorted.bam Indexed_bam=/path/to/sorted.bam.bai

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Peak Calling and Annotation in SCRAP for Small Noncoding RNA: Target RNA Interaction Studies (Video) | JoVE

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