identification of A-to-I RNA Editing

1. Quality Contorl of Fastq

2. Alignment to Reference Genome

   Recommended use STAR-2pass to mapping reads to genome

3. Pre-process of Bam File

   remove multi aglin, duplicate reads, splitN, and so on

   Detailed operation can refer: https://software.broadinstitute.org/gatk/documentation/article.php?id=3891

4. use GATK to call candidate site

5. Basic Variant filtering(optional)

6. Identification of editing sites

   • Select single nucleotide variants(SNV) from all variant results , use snpEff to annot SNV
   • Select A>T changes in the gene interval, depending on the direction of gene transcription
   • Remove sites that appear in Cosmic, dbSNP, TCGA somatic mutations database
   • Remove sites which the editing level is 1.0 in all sample
   • At least 10 reads in at least 1 sample
   • RNA editing sites is exists at least 2 sample

ref：

• The Genomic Landscape and Clinical Relevance of A-to-I RNA Editing in Human Cancers
• Dynamic regulation of RNA editing in human brain development and disease
• A disrupted RNA editing balance mediated by ADARs (Adenosine DeAminases that act on RNA) in human hepatocellular carcinoma
• ADAR1 promotes malignant progenitor reprogramming in chronic myeloid leukemia
• Genome-wide analysis of A-to-I RNA editing by single-molecule sequencing in Drosophila