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In this lab, we'll look at how to identify enriched gene ontology (GO) terms. For For this analysis, we'll be using the differential analysis results we generated using DESeq.
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Enrichment test: whether “DEG list” contain contains more representatives of a certain GO category than expected by chance (Fisher’s exact, hypergeometric, or similar test).
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SCP THE DATA OVER TO YOUR COMPUTER:
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#ON stampede2ls6: copy the path for the ALL and DEG files pwd #ON LOCAL COMPUTER: from a terminal tab scp <username>@stampede2<username>@ls6.tacc.utexas.edu:<pathtofileson/DEG> . scp <username>@stampede2<username>@ls6.tacc.utexas.edu:<pathtofileson/ALL> . |
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##Command to pull out ALL gene ids, sorted by adjpvalue store it in a file called ALLRANKED #Remember we already sorted our results by adjusted pvalue in the deseq2 script before writing it out to a file. So #you just need to pull out the gene ids in the order it already is in. sed 's/,/\t/g' deseq2_htseq_C1_vs_C2.csv|cut -f 1|sed 's/"//g'|grep '^FB' > ALLRANKED |
SCP THE DATA OVER TO YOUR COMPUTER:
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#ON stampede2ls6: copy the path for the ALLRANKED file pwd #ON LOCAL COMPUTER: from a terminal tab scp <username>@stampede2<username>@ls6.tacc.utexas.edu:<pathtofileson/ALLRANKED> . |
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RUN GORILLA USING THE RANKED METHOD: http://cbl-gorilla.cs.technion.ac.il/
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