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PairedEnd_noMIDs_Tutorial.md

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Paired End no MIDs/Barcodes Tutorial

Source: https://seekdeep.brown.edu/tutorial_PairedEnd_noMIDs.html

Navigate to your Directory

cd ~/SeekDeep

Get sample file (no replicates)

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

Download genomes if they haven't been before

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

Set up command

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

Run analysis with whatever number of CPUs you want to use (below is 8)

./runAnalysis.sh 8

Start data viewer

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

Then, navigate to localhost on your local browser. You should then be able to see the viewer tool.

Use Pipeline Wrapper

cd ..

SeekDeep setupTarAmpAnalysis --samples sampleNames.tab.txt --outDir analysis_output --inputDir fastq/ --idFile ids.tab.txt --overlapStatusFnp overlapStatuses.txt --lenCutOffs lenCutOffs.txt "--extraExtractorCmds=--checkRevComplementForPrimers" --groupMeta metaData.tab.txt

Results are in the SeekDeep/CamThaiGhanaDRC_2011_2013_drugRes_withRevComp/analysis/popClustering/ folder where each directory is a gene. (e.g. PfAMA1-129-279/analysis/selectedClustersInfo.tab.txt)