Example Run¶

This page provides documentation for an example run of with sample dataset based on alignment to Drosophila (dm6). Load the dataset into mysql table and identify RNA editing sites. This assumes that load_matrix_data.pl and find_rnaeditsites.pl has been setup properly.

#path of the examples files
cd /path_from_root/HyperTRIBE/examples/
#unzip the compressed files
gunzip *.gz
# prepare the annotation files for drosophila dm6
cd /path_from_root/HyperTRIBE/annotations/
gunzip *.gz

Open load_table.sh to update the HyperTRIBE_DIR variable

#path of HyperTRIBE code
HyperTRIBE_DIR="/path_from_root/HyperTRIBE/CODE"

Open rnaedit_wtRNA_RNA.sh to update the HyperTRIBE_DIR variable

#path of HyperTRIBE code
HyperTRIBE_DIR="/path_from_root/HyperTRIBE/CODE"
#set the location of the annotation file
annotationfile="/path_from_root/HyperTRIBE/annotations/refFlat.txt

Now, load the data to MySQL and run the shell scripts. This script converts the SAM file to matrix and then loads the data into MySQL tables.

#upload data to mysql tables, one for RNA and one gDNA
#1. First argument alignment SAM file
#2. mysql tablename
#3. Expt name
#4. Timepoint/Replicate Integer
./load_table.sh S2_wtRNA_chr2L.sort.sam exampleDB wtRNA 1
./load_table.sh HyperTRIBE_rep1_chr2L.sort.sam exampleDB HyperTRIBE 2
#

Now identify the editing sites with rnaedit_wtRNA_RNA.sh. If you changed the arguments of the loadPtable.sh script, please update the relevant variables in rnaedit_wtRNA_RNA.sh before running that script.

./rnaedit_wtRNA_RNA.sh

This should produce an output file called HyperTRIBE_1_2_A2G.bedgraph, where 3712 RNA editing sites are identified. You can also log into mysql to see how the files, S2_wtRNA_chr2L.sort.matrix & HyperTRIBE_rep1_chr2L.sort.matrix, have populated the mysql tables.