PairedEnd_noMIDs_script

cd ~/SeekDeep

wget http://seekdeep.brown.edu/data/SeekDeepTutorialData/ver2_6_0/CamThaiGhanaDRC_2011_2013_drugRes_withRevComp.tar.gz --no-check-certificate 
tar -zxvf CamThaiGhanaDRC_2011_2013_drugRes_withRevComp.tar.gz

cd CamThaiGhanaDRC_2011_2013_drugRes_withRevComp

wget http://seekdeep.brown.edu/data/plasmodiumData/pfgenomes.tar.gz --no-check-certificate 
tar -zxvf pfgenomes.tar.gz

SeekDeep genTargetInfoFromGenomes --gffDir pfgenomes/info/gff --genomeDir pfgenomes/genomes/ --primers ids.tab.txt --numThreads 4 --pairedEndLength 250 --dout extractedRefSeqs

SeekDeep setupTarAmpAnalysis --samples sampleNames.tab.txt --outDir analysis --inputDir fastq/ --idFile ids.tab.txt --overlapStatusFnp extractedRefSeqs/forSeekDeep/overlapStatuses.txt --lenCutOffs extractedRefSeqs/forSeekDeep/lenCutOffs.txt --refSeqsDir extractedRefSeqs/forSeekDeep/refSeqs "--extraExtractorCmds=--checkRevComplementForPrimers" --groupMeta metaData.tab.txt

cd analysis

./runAnalysis.sh 8

SeekDeep popClusteringViewer --verbose --configDir "$(pwd)/serverConfigs" --bindAddress 0.0.0.0 --port 9881 --name pcv