Changes between Version 17 and Version 18 of SOPs/rna-seq-diff-expressions


Ignore:
Timestamp:
01/15/14 14:33:10 (11 years ago)
Author:
gbell
Comment:

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  • SOPs/rna-seq-diff-expressions

    v17 v18  
    4040         * To request a certain amount of memory and a specific node use ''bsub  -R "rusage[mem=50000]" -m NodeName ''
    4141    * Remove the rows at the bottom with descriptions like no_feature, ambiguous, etc.
    42     * For custom analyses, you can add a pseudocount (such as 1) to all genes in all samples to prevent log2 ratios that require dividing by 0 and reduce background count noise -- BUT be aware that some statistical methods (like DESeq) require raw input values without any pseudocounts or normalization.
     42    * For custom analyses, you can add a pseudocount (such as 1 or another small number) to all genes in all samples to prevent log2 ratios that require dividing by 0 and reduce background count noise -- BUT be aware that some statistical methods (like DESeq) require raw input values without any pseudocounts or normalization.
    4343
    4444  * **Quantification of FPKM values**
    … …  
    5454
    5555  * **Gene filtering**
    56     * Remove from the analysis any genes with 0 counts.
     56    * Remove from the analysis any genes with 0 counts across all samples.  Some analysis tools do this themselves.
    5757    * Remove counts for any genes we want to classify as contaminants or simply "not interesting" such as ribosomal RNAs (if these are included in the GTF gene annotation file).
    5858