Changes between Version 16 and Version 17 of SOPs/go_annotation

Timestamp:

09/28/20 14:29:51 (4 years ago)

Author:

ibarrasa

Comment:

--

SOPs/go_annotation

@@ -29 +29 @@
      * 3. Select one of the gene sets from the "Gene sets database". We recommend starting with the Hallmarks set (h.all). You can find more information about the sets [[https://www.gsea-msigdb.org/gsea/msigdb/index.jsp|here ]]
      * 4. Select your uploaded ranked list and click the run button.  
-   3. To run the same type of analysis on the command line, you can see the command the GUI used clicking the "Command" button and run that command in your Linux machine.
+   3. To run the same type of analysis on the command line, you can see the command the GUI used clicking the "Command" button and run that command in your Linux machine. You will need java 11. For Whitehead users: switch to java 11 with this command "ml java/10" (after this if you run "java --version" you will get "openjdk 11.0.8 2020-07-14")
 {{{
-java -Xmx512m -cp /usr/lib/share/gsea2/gsea2-2.2.2.jar xtools.gsea.GseaPreranked -gmx gseaftp.broadinstitute.org://pub/gsea/gene_sets/h.all.v5.2.symbols.gmt -collapse false -mode Max_probe -norm meandiv -nperm 1000 -rnk ./MY_COMPARISON.rnk -scoring_scheme weighted -rpt_label GSEA_out_v1 -chip gseaftp.broadinstitute.org://pub/gsea/annotations/GENE_SYMBOL.chip -include_only_symbols true -make_sets true -plot_top_x 20 -rnd_seed timestamp -set_max 500 -set_min 2 -zip_report false -out GSEA_OUT.TEST_v1 -gui false
+gsea-cli.sh GSEAPreranked -gmx ftp.broadinstitute.org://pub/gsea/gene_sets/h.all.v7.2.symbols.gmt -norm meandiv -nperm 1000 -rnk myFile.rnk -scoring_scheme weighted -rpt_label my_analysis -create_svgs false -make_sets true -plot_top_x 20 -rnd_seed timestamp -set_max 500 -set_min 15 -zip_report false -out ./output/sep28
 }}}
-   ==== Fast gene set enrichment analysis (fgsea) ====
-[https://bioconductor.org/packages/release/bioc/vignettes/fgsea/inst/doc/fgsea-tutorial.html/ fgsea]
    ==== Unranked List ====
  
@@ -42 +40 @@
   1.  Use MSigDB for gene sets or create custom gene sets in correct format
   1.  Run GSEA, use default options to start
+
+
+   ==== Fast gene set enrichment analysis (fgsea) ====
+[https://bioconductor.org/packages/release/bioc/vignettes/fgsea/inst/doc/fgsea-tutorial.html/ fgsea]
 
    ==== Single-sample GSEA (ssGSEA) ====