Name | Modified | Size | Downloads / Week |
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annotations | 2016-04-14 | ||
ReAnnotator_1-0-0.tar.gz | 2014-04-09 | 11.1 kB | |
README.txt | 2014-04-09 | 2.8 kB | |
README.doc | 2014-04-09 | 30.7 kB | |
Totals: 4 Items | 44.7 kB | 1 |
######################################## # HOW TO GET STARTED WITH RE-ANNOTATOR # ######################################## A. Things to do before the first time using Re-Annotator I) Install External Programs Following programs should be installed on your system prior to running the Re-Annotator: a) PERL b) BWA (http://sourceforge.net/projects/bio-bwa/files/) c) SAMtools (https://sourceforge.net/projects/samtools/files/) d) Annovar (http://www.openbioinformatics.org/annovar/) II) Get External Data a) Reference Genome Sequence - Download the reference genome, e.g., hg19 http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz - unzip (using gzip) make sure every chromosome is in a single file b) Gene Database - Download information on gene locations, e.g., RefSeq http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz - unzip (using gzip) c) Make sure desired databases for annotation are available in Annovar: These can be for instance - RefGene ./annotate_variation.pl -downdb refGene -buildver hg19 humandb/ - snpdatabase, e.g., snp129 (available from annovar) ./annotate_variation.pl -downdb snp129 -buildver hg19 -webfrom annovar humandb/ III) Generate the mRNA Reference Sequence a) Execute new_exomeBuilding.pl to build the mRNA reference sequence example: $> ./BuildExomeReference.pl -i ~/ReAnnotator/refGene.txt -o ~/ReAnnotator/exomeRef/hg19exome -r ~/ReAnnotator/hg19/ b) Use "BWA index" to generate the BWA index files for i) the exome reference sequence ii) the whole genome reference sequence IV) Complete the config.sh * provide exact locations to the external programs in the file config.sh * config.sh is also the place to change the default settings - # of CPUs - # of mismatches - genome version, e.g., gh19, hg18, mm9, ... - genedb (refGene, ensemble, ...) - snpdb (snp135, snp136, ...) NOTE: step III) has to be carried out every time the Gene Database is updated! NOTE: update config.sh to meet the needs for your Re-Annotation B. Things to do at every run I) Check that config.sh is set up correctly for the genome and exome you are about to use - regenerate the mRNA reference if you are using an updated database version or new genome release II) Convert probes file into a fasta file For Illumina probe files the script parse_fastaFromOriginIlmnAnno.pl can be used. III) execute: ./ReAnnotator.sh with corresponding parameters example: ./ReAnnotator.sh my_illumina_probes.fasta ~/ReAnnotator/exomeRef/hg19exome_inclUTR.fasta ~/ReAnnotator/hg19/hg19genome.fasta.gz ~/ReAnnotator/refGene.txt ~/ReAnnotator/outputs/ ~/ReAnnotator/tmp/ Prior to running the script, make sure that all the directories exist. The script will call following scripts in a row: a) run_realignment.sh b) run_coordinateConversion.sh c) run_genome_snp_annotation.sh