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Fiumara_BasePrimeEd2022
Fiumara_BasePrimeEd2022_RNAseq
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1fe8ac2a
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authored
Jul 25, 2023
by
Stefano Beretta
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@@ -18,7 +18,7 @@ RNA-seq analysis to compare Treated (BE4, ABE8, Cas9, Mock electro) vs Untreated
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@@ -18,7 +18,7 @@ RNA-seq analysis to compare Treated (BE4, ABE8, Cas9, Mock electro) vs Untreated
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Post-analyses with the R/Bioconductor package _ClusterProfiler_ using the Hallmark collection from _MSigDB_ as reference database
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Post-analyses with the R/Bioconductor package _ClusterProfiler_ using the Hallmark collection from _MSigDB_ as reference database
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Visualization of the (spliced) alignments on the TP73 gene was done with Integrative Genomes Viewer (_IGV_).
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Visualization of the (spliced) alignments on the TP73 gene was done with Integrative Genomes Viewer (_IGV_).
Variant calling analysis on RNA-Seq base editing data:
Variant calling analysis on RNA-Seq base editing data
(GSE218462)
:
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Merging of reads from replicates of each condition and downsampling to 120M with _Seqtk_
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Merging of reads from replicates of each condition and downsampling to 120M with _Seqtk_
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Alignment to the human genome assembly (GRCh38) with _STAR_
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Alignment to the human genome assembly (GRCh38) with _STAR_
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Mark duplicates with _Picard MarkDuplicates_ and split of eads containing Ns with _GATK SplitNCigarReads_
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Mark duplicates with _Picard MarkDuplicates_ and split of eads containing Ns with _GATK SplitNCigarReads_
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