Changes between Version 2 and Version 3 of SOPs/geneFeatureHeatmaps


Ignore:
Timestamp:
07/19/13 12:16:38 (11 years ago)
Author:
gbell
Comment:

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  • SOPs/geneFeatureHeatmaps

    v2 v3  
    1616     * The BaRC script /nfs/BaRC_Public/BaRC_code/Perl/split_genome_regions_into_windows.pl can do this.
    1717  1. Quantify reads that map to each window of each region.
    18      * Method 1: Use coverageBed (ex: coverageBed -abam accepted_hits.bam -b region.windows.bed > out)
     18     * Method 1: Use coverageBed (ex: coverageBed -split -abam accepted_hits.bam -b region.windows.bed > out)
    1919     * Method 2: Use cufflinks (after converting region.windows.bed into a GTF file)
    2020     * Other methods?