Removes shRNAs with low read counts in original DNA plasmid pool. Outputs a GCT file containing filtered shRNA data and a GCT file containing the mean read count for each shRNA in the original DNA plasmid pool.
Author: Barbara Weir, Sara Howell;The Broad Institute
FilterLowshRNAs is a GenePattern module that implements a quality control step during the analysis of shRNA pooled screen data. The user inputs at least one and up to three GCT files containing shRNA data, with each file containing data from a separate batch. The cell lines where the shRNAs have low read counts in the original DNA plasmid pool are defined as NaN in each file and shRNAs where the read counts in the original DNA plasmid pool were low in all files are removed from the dataset entirely.
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|shRNA data file(s) *||Format is a GCT file where each row corresponds to a unique shRNA sequence. At least one file is required and up to three files can be uploaded.|
|File Prefix *||User-defined prefix of output file names.|
* - required
Memory Requirements on the GenePattern Server: 8G
|30||2014-09-16||updated command line|
|29||2014-04-11||Converted documentation from pdf to html|