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blockclust.xml tool_dependencies.xml |
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| diff -r 27dde42069e0 -r 49e600128a73 blockclust.xml --- a/blockclust.xml Tue Jul 08 13:18:16 2014 -0400 +++ b/blockclust.xml Wed Jul 09 08:38:01 2014 -0400 |
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| @@ -161,9 +161,12 @@ fast graph-kernel techniques. BlockClust allows both clustering and classification of small non-coding RNAs. -BlockClust runs in three modes: +BlockClust runs in three operating modes: + 1) Pre-processing - converts given mapped reads (BAM) into BED file of tags -2) Clustering and classification - of given input block groups (from blockbuster tool) as explained in the original paper. + +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. For a thorough analysis of your data, we suggest you to use complete blockclust workflow, which contains all three modes of operation. @@ -171,31 +174,33 @@ **Inputs** BlockClust input files are dependent on the mode of operation: -1) Pre-processing mode: -Binary Sequence Alignment Map (BAM) file + +1. Pre-processing mode: + * Binary Sequence Alignment Map (BAM) file -2) Clustering and classification: -A blockgroups file generated by blockbuster tool -Select reference genome +2. Clustering and classification: + * A blockgroups file generated by blockbuster tool + * Select reference genome -3) Post-processing: -Output of cmsearch, searched clusters generated by BlockClust against Rfam -BED file containing clusters generated by BlockClust -Pairwise similarities of blockgroups generated by BlockClust +3. Post-processing: + * Output of cmsearch, searched clusters generated by BlockClust against Rfam + * BED file containing clusters generated by BlockClust + * Pairwise similarities of blockgroups generated by BlockClust -**Output** -1) Pre-processing mode: -BED file of tags with expressions +**Outputs** + +1. Pre-processing mode: + * BED file of tags with expressions -2) Clustering and classification: -Hierarchical clustering plot of all input blockgroups by their similarity -Pairwise similarities of all input blockgroups -BED file containing predicted clusters -BED file containing prediction of blockgroups by pre-compiled SVM binary classification model. +2. Clustering and classification: + * Hierarchical clustering plot of all input blockgroups by their similarity + * Pairwise similarities of all input blockgroups + * BED file containing predicted clusters + * 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 -hierarchical clustering made out of centroids of each BlockClust predicted cluster +3. Post-processing: + * Distribution of clusters with annotations searched against Rfam database + * Hierarchical clustering made out of centroids of each BlockClust predicted cluster ------ |
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| diff -r 27dde42069e0 -r 49e600128a73 tool_dependencies.xml --- a/tool_dependencies.xml Tue Jul 08 13:18:16 2014 -0400 +++ b/tool_dependencies.xml Wed Jul 09 08:38:01 2014 -0400 |
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| @@ -70,21 +70,21 @@ </action> <action type="make_directory">$INSTALL_DIR/data/annotations</action> <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/dm3.tar.gz</action> - <action type="shell_command">tar xfvz dm3.tar.gz -C $INSTALL_DIR/data/annotations/</action> + <action type="shell_command">cd ..; tar xfvz dm3.tar.gz -C $INSTALL_DIR/data/annotations/</action> <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/hg19.tar.gz</action> - <action type="shell_command">tar xfvz hg19.tar.gz -C $INSTALL_DIR/data/annotations/</action> + <action type="shell_command">cd ..; tar xfvz hg19.tar.gz -C $INSTALL_DIR/data/annotations/</action> <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/mm10.tar.gz</action> - <action type="shell_command">tar xfvz mm10.tar.gz -C $INSTALL_DIR/data/annotations/</action> + <action type="shell_command">cd ..; tar xfvz mm10.tar.gz -C $INSTALL_DIR/data/annotations/</action> <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/panTro4.tar.gz</action> - <action type="shell_command">tar xfvz panTro4.tar.gz -C $INSTALL_DIR/data/annotations/</action> + <action type="shell_command">cd ..; tar xfvz panTro4.tar.gz -C $INSTALL_DIR/data/annotations/</action> <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/rheMac3.tar.gz</action> - <action type="shell_command">tar xfvz rheMac3.tar.gz -C $INSTALL_DIR/data/annotations/</action> + <action type="shell_command">cd ..; tar xfvz rheMac3.tar.gz -C $INSTALL_DIR/data/annotations/</action> <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/celWS235.tar.gz</action> - <action type="shell_command">tar xfvz celWS235.tar.gz -C $INSTALL_DIR/data/annotations/</action> + <action type="shell_command">cd ..; tar xfvz celWS235.tar.gz -C $INSTALL_DIR/data/annotations/</action> <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/tair10.tar.gz</action> - <action type="shell_command">tar xfvz tair10.tar.gz -C $INSTALL_DIR/data/annotations/</action> + <action type="shell_command">cd ..; tar xfvz tair10.tar.gz -C $INSTALL_DIR/data/annotations/</action> <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/models.tar.gz</action> - <action type="shell_command">tar xfvz models.tar.gz -C $INSTALL_DIR/data/</action> + <action type="shell_command">cd ..; tar xfvz models.tar.gz -C $INSTALL_DIR/data/</action> <action type="set_environment"> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> <environment_variable action="set_to" name="BLOCKCLUST_DATA_PATH">$INSTALL_DIR/data</environment_variable> |