Mercurial > repos > rnateam > blockclust
changeset 6:6721468f2f9f draft
Uploaded
| author | rnateam |
|---|---|
| date | Wed, 09 Jul 2014 13:01:56 -0400 |
| parents | a50bd507edfe |
| children | e6f49ee3509c |
| files | blockclust.xml |
| diffstat | 1 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/blockclust.xml Wed Jul 09 12:35:26 2014 -0400 +++ b/blockclust.xml Wed Jul 09 13:01:56 2014 -0400 @@ -65,7 +65,7 @@ cp #echo os.path.join($outputdir, 'hclust_tree.pdf')# $hclust_plot; cp #echo os.path.join($outputdir, 'discretized.gspan.tab')# $sim_tab_out #elif str($tool_mode.operation) == "post": - BlockClustPipeLine.pl -m POST -cbed $tool_mode.clusters_bed -cm $tool_mode.cmsearch_out -tab $tool_mode.sim_tab_in -o ./; + BlockClustPipeLine.pl -m POST -cbed $tool_mode.clusters_bed -cm $tool_mode.cmsearch_out -tab $tool_mode.sim_tab_in -rfam \$BLOCKCLUST_DATA_PATH/rfam_map.txt -o ./; #end if </command> <inputs> @@ -167,7 +167,7 @@ 2) Clustering and classification - of given input blockgroups (output of blockbuster tool) as explained in the original paper. -3) Post-processing - extracts distribution of clusters searched against Rfam database and plots hierarchical clustering made out of centroids of each BlockClust predicted cluster. +3) Post-processing - plots for overview of predicted clusters. For a thorough analysis of your data, we suggest you to use complete blockclust workflow, which contains all three modes of operation. @@ -199,7 +199,7 @@ * BED file containing prediction of blockgroups by pre-compiled SVM binary classification model. 3. Post-processing: - * Distribution of clusters with annotations searched against Rfam database + * Plot of distribution of ncRNA families per predicted cluster (overview of cluster precissions). The annotation of ncRNA families are retrieved by searching cluster instances against Rfam database. * Hierarchical clustering made out of centroids of each BlockClust predicted cluster ------