1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/144e064fa5c5/ changeset: r5079:144e064fa5c5 user: jgoecks date: 2011-02-17 20:25:56 summary: Set default value for Cuffdiff's minimum alignment count parameter to reflect v0.9.3 affected #: 1 file (3 bytes)

--- a/tools/ngs_rna/cuffdiff_wrapper.xml Thu Feb 17 13:57:38 2011 -0500 +++ b/tools/ngs_rna/cuffdiff_wrapper.xml Thu Feb 17 14:25:56 2011 -0500 @@ -90,7 +90,7 @@

<param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/><param name="min_mapqual" type="integer" value="0" label="Min SAM Mapping Quality" help="Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number."/> - <param name="min_alignment_count" type="integer" value="0" label="Min Alignment Count" help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/> + <param name="min_alignment_count" type="integer" value="1000" label="Min Alignment Count" help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/><param name="do_normalization" type="select" label="Perform quartile normalization" help="Removes top 25% of genes from FPKM denominator to improve accuracy of differential expression calls for low abundance transcripts."><option value="No">No</option><option value="Yes">Yes</option>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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