Changes between Version 27 and Version 28 of SOPs/go_annotation


Ignore:
Timestamp:
01/12/21 13:10:55 (4 years ago)
Author:
thiruvil
Comment:

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  • SOPs/go_annotation

    v27 v28  
    88* Instructions for using DAVID can be found under //Functional Annotation// on the DAVID web site.
    99* You'll probably end up running DAVID multiple times, with different types of annotations, to get the more informative combination.
    10 * Full output can be downloaded and viewed as a spreadsheet.
     10* More details:
     11    * DAVID has an upper limit of 3000 genes as input
     12    * Full output can be downloaded as text and viewed as a spreadsheet.
     13    * By default, DAVID uses the entire genome (annotation) as background, if your background is different make sure to enter/change the background, e.g. if using a microarray study the background gene list would be all the genes/probsets assayed.
     14    * [[https://david.ncifcrf.gov/helps/update.html| DAVID Knowledgebase]] and [[https://academic.oup.com/view-large/82532053| annotation ]] contains information of the databases or sources used by DAVID
    1115
    1216=== Gene Set Enrichment Analysis (GSEA) ===
    … …  
    2731   1. Create a two column file with gene names as first column and numeric values for second column (eg. log2 fold change, log2 ratio). The file does not need to be sorted and it should have extension ".rnk".
    2832     * The second column, used to rank genes, could be log2 fold change, t-statistic, or another scoring scheme that takes into account both log ratio and p-value.
    29    2. To run using the GUI
    3033
    31      * 1. Start GSEA. On tak, the command is 'gsea'.
    32      * 2. Upload your ranked file "file.rnk". Click on "Steps in GSEA analysis -> Load data" 
    33      * 3. Click on  "Tools -> GseaPreranked" 
    34      * 4. 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 ]]
    35      * 5. Select your uploaded ranked list and click the run button. 
    36    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.
     34   2. Run GSEA:
     35
     36     *  To run using the GUI
     37        * 1. Start GSEA. On tak, the command is 'gsea'.
     38        * 2. Upload your ranked file "file.rnk". Click on "Steps in GSEA analysis -> Load data" 
     39        * 3. Click on  "Tools -> GseaPreranked" 
     40        * 4. 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 ]]
     41        * 5. Select your uploaded ranked list and click the run button.
     42
     43     *  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.
    3744{{{
    3845gsea-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