Mercurial > repos > rnateam > blockclust
comparison blockclust.xml @ 3:27dde42069e0 draft
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author | rnateam |
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date | Tue, 08 Jul 2014 13:18:16 -0400 |
parents | f973ec6e5192 |
children | 49e600128a73 |
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2:f973ec6e5192 | 3:27dde42069e0 |
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161 fast graph-kernel techniques. BlockClust allows both clustering and | 161 fast graph-kernel techniques. BlockClust allows both clustering and |
162 classification of small non-coding RNAs. | 162 classification of small non-coding RNAs. |
163 | 163 |
164 BlockClust runs in three modes: | 164 BlockClust runs in three modes: |
165 1) Pre-processing - converts given mapped reads (BAM) into BED file of tags | 165 1) Pre-processing - converts given mapped reads (BAM) into BED file of tags |
166 2) Clustering and classification - of given input block groups (from blockbuster tool) as explained in [1]_ | 166 2) Clustering and classification - of given input block groups (from blockbuster tool) as explained in the original paper. |
167 3) Post-processing - extracts distribution of clusters searched against Rfam database and plots hierarchical clustering made out of centroids of each BlockClust predicted cluster. | 167 3) Post-processing - extracts distribution of clusters searched against Rfam database and plots hierarchical clustering made out of centroids of each BlockClust predicted cluster. |
168 | 168 |
169 For a thorough analysis of your data, we suggest you to use complete blockclust workflow, which contains all three modes of operation. | 169 For a thorough analysis of your data, we suggest you to use complete blockclust workflow, which contains all three modes of operation. |
170 | 170 |
171 **Inputs** | 171 **Inputs** |
197 Distribution of clusters with annotations searched against Rfam database | 197 Distribution of clusters with annotations searched against Rfam database |
198 hierarchical clustering made out of centroids of each BlockClust predicted cluster | 198 hierarchical clustering made out of centroids of each BlockClust predicted cluster |
199 | 199 |
200 ------ | 200 ------ |
201 | 201 |
202 **Licenses** | |
203 | |
204 If **BlockClust** is used to obtain results for scientific publications it should be cited as [1]_. | |
205 | |
206 **References** | 202 **References** |
207 | 203 |
208 [1] Pavankumar Videm, Dominic Rose, Fabrizio Costa, and Rolf Backofen. "BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles." Bioinformatics 30, no. 12 (2014): i274-i282. | 204 Pavankumar Videm, Dominic Rose, Fabrizio Costa, and Rolf Backofen. "BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles." Bioinformatics 30, no. 12 (2014): i274-i282. |
209 | 205 |
210 | 206 |
211 </help> | 207 </help> |
212 </tool> | 208 </tool> |