Download indexes and annotations

RNAEditor requires a set of annotation files and databases to detect editing sites. Either download one of the following annotation bundles or download the files manually by executing the commands below.

Human
Mouse

Unix commands to download GRCH38 manually
  • Reference Genome:
    • wget -qO- ftp://ftp.ensembl.org/pub/release-83/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz |gunzip -c > Homo_sapiens.GRCh38.dna.primary_assembly.fa bwa index Homo_sapiens.GRCh38.dna.primary_assembly.fa; samtools faidx Homo_sapiens.GRCh38.dna.primary_assembly.fa
  • Create Dictionary of Reference genome:
    • java -jar /usr/local/bin/picard-tools/CreateSequenceDictionary.jar REFERENCE=Homo_sapiens.GRCh38.dna.primary_assembly.fa OUTPUT=Homo_sapiens.GRCh38.dna.primary_assembly.dict
  • Gene Annotation:
    • wget -qO- ftp://ftp.ensembl.org/pub/release-83/gtf/homo_sapiens/Homo_sapiens.GRCh38.83.gtf.gz |gunzip -c > Homo_sapiens.GRCh38.83.gtf
  • dbSNP Database:
    • wget -qO- ftp://ftp.ensembl.org/pub/release-83/variation/vcf/homo_sapiens/Homo_sapiens.vcf.gz |gunzip -c |awk 'BEGIN{FS="\t";OFS="\t"};match($5,/\./){gsub(/\./,"N",$5)};$5 == "" && $1 !~ /^#/ {gsub("","N",$5)};$3 ~ /rs193922900/ {$5="TN"};$3 ~ /rs59736472/ {$5="AN"};$5 ~ /H/ {gsub(/H/,"N",$5)};{print $0}' dbSNP.vcf
  • ESP Database:
    • wget -qO- ftp://ftp.ensembl.org/pub/release-83/variation/vcf/homo_sapiens/ESP65*.vcf.gz |gunzip -c |grep -v ^## |grep -v rs[0-9][0-9] > ESP.vcf
  • HAPMAP Database:
    • wget -qO- ftp://ftp.ensembl.org/pub/release-83/variation/vcf/homo_sapiens/*HAPMAP*.vcf.gz |gunzip -c |grep -v ^## |grep -v rs[0-9][0-9] > HAPMAP.vcf
  • Download Alu Regions:
    • #download Alu regions from the repeat masker
      • Link: http://genome.ucsc.edu/cgi-bin/hgTables
      • group: Variation and Repeats
      • track: RepeatMasker
      • table: rmsk
      • output format: BED
    #run this awk command to make the alu region compatible to the ensemble annotation
    awk 'BEGIN{FS="\t";OFS="\t"} match($1,/chr/){$1 = substr($1,4)}{print $0}' yourFile.bed > youFile_noCHR.bed