Add-ons intro

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After you complete the initial installation you will have the base ExpressionPlot system but won't be able to do any analysis until you add in some data. This is done easily with the EP-manage.pl script to do this (located in the util/ subdirectory of the ExpressionPlot home).

If you are only running the front-end (you have your own back-end), then strictly speaking you could get away without adding anything on, but you would of course have to populate the database by other methods. Even so, it might be useful to download at least an annotation for the genome that you are using so that the SeqView Tool can show known transcripts along with your data.

One way to just try out ExpressionPlot is to get it running on some human tissue panel data. Here is a sequence of add-ons that should populate your database with some the processed data (the download for hg18 annotation is about 70MB and for the tissue panel is about 600MB so it may take a little while):

# Go to ExpressionPlot util directory
cd `expressionplot-config`/util

# Get hg18 annotation files
./EP-manage.pl get_annot hg18

# Get processed Human Tissue Panel data
./EP-manage.pl get_project Human_Tissue_Panel_processed

If you want to try out the back-end, then you could download the raw sequencing data instead of the processed data. This download is bigger (1.6GB), and you still will need the annotation files. These commands will download the annotation and the raw data, then start the pipeline:

# Go to ExpressionPlot util directory
cd `expressionplot-config`/util

# Get hg18 annotation files
./EP-manage.pl get_annot hg18

# Get Human Tissue Panel sequences
./EP-manage.pl get_project Human_Tissue_Panel

# Start up screen (optional)
screen -S EP-pipeline-on-Tissue-Panel

# Start pipeline
EP=`expressionplot-config`
cd $EP/projects/Human_Tissue_Panel
$EP/RNASeq/RNASeq-pipeline.pl lanes.txt hg18 -j hg18_all_junctions -hjl 31 \
  -cl $EP/annot/hg18/hg18_trimmed_gene_clusters.tsv \
  -ae $EP/annot/hg18/hg18_acembly_AE_events_with_flanking_SS.tsv \
  -p iDEA -l pipeline.%d%b%y.log \
  -ri $EP/annot/hg18/hg18_acembly_intron_events.xls \
  -ate $EP/annot/hg18/hg18_ensGene_term_exons.tsv \
  -ensT $EP/annot/hg18/hg18_ensembl_and_tRNA_clusters.tsv \
  -admin expressionplot -l pipeline.%d%b%y.log \

Then point your web browser to http://SERVERNAME/cgi-bin/expressionplot/home.pl and you are ready to go!


See Installing add-ons for more details.