Commit 1fe8ac2a authored by Stefano Beretta's avatar Stefano Beretta
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Update README.md

parent 81fea2c5
...@@ -18,7 +18,7 @@ RNA-seq analysis to compare Treated (BE4, ABE8, Cas9, Mock electro) vs Untreated ...@@ -18,7 +18,7 @@ RNA-seq analysis to compare Treated (BE4, ABE8, Cas9, Mock electro) vs Untreated
- Post-analyses with the R/Bioconductor package _ClusterProfiler_ using the Hallmark collection from _MSigDB_ as reference database - Post-analyses with the R/Bioconductor package _ClusterProfiler_ using the Hallmark collection from _MSigDB_ as reference database
- Visualization of the (spliced) alignments on the TP73 gene was done with Integrative Genomes Viewer (_IGV_). - 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):
- Merging of reads from replicates of each condition and downsampling to 120M with _Seqtk_ - Merging of reads from replicates of each condition and downsampling to 120M with _Seqtk_
- Alignment to the human genome assembly (GRCh38) with _STAR_ - Alignment to the human genome assembly (GRCh38) with _STAR_
- Mark duplicates with _Picard MarkDuplicates_ and split of eads containing Ns with _GATK SplitNCigarReads_ - Mark duplicates with _Picard MarkDuplicates_ and split of eads containing Ns with _GATK SplitNCigarReads_
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