annotate blockclust.xml @ 9:57f66041cc0f draft

Uploaded
author rnateam
date Sun, 21 Sep 2014 23:00:44 -0400
parents c1cc480c53da
children 24d09ba85e45
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
1 <tool id="blockclust" name="BlockClust" version="1.0.0">
2
f973ec6e5192 Uploaded
rnateam
parents: 1
diff changeset
2 <description>efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles</description>
0
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
3 <requirements>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
4 <requirement type="package" version="1.0">blockclust</requirement>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
5 <requirement type="package" version="1.1">eden</requirement>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
6 <requirement type="package" version="3.0.1">R_3_0_1</requirement>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
7 <requirement type="package" version="0.1.19">samtools</requirement>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
8 <requirement type="package" version="12.135">mcl</requirement>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
9 <requirement type="package" version="1.0">blockclust_rlibs</requirement>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
10 </requirements>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
11 <version_command>echo '1.0'</version_command>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
12 <command>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
13 #if str($tool_mode.operation) == "pre":
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
14 BlockClustPipeLine.pl -m PRE -bam $tool_mode.reads_bam -tbed $tags_bed
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
15 #elif str($tool_mode.operation) == "clust":
1
a92d8689aa30 Uploaded
rnateam
parents: 0
diff changeset
16 #set $outputdir = $clusters.files_path
0
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
17 #set $accept_bed=list()
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
18 #set $reject_bed=list()
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
19 ## prepare annotations
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
20 #if str($tool_mode.reference) == "hg19":
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
21 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.accept.bed")
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
22 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.reject.bed")
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
23 #elif str($tool_mode.reference) == "mm10":
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
24 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.accept.bed")
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
25 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.reject.bed")
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
26 #elif str($tool_mode.reference) == "dm3":
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
27 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.accept.bed")
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
28 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.reject.bed")
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
29 #elif str($tool_mode.reference) == "rheMac3":
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
30 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/rheMac3/rheMac3.accept.bed")
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
31 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/rheMac3/rheMac3.reject.bed")
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
32 #elif str($tool_mode.reference) == "panTro4":
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
33 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/panTro3/panTro4.accept.bed")
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
34 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/panTro3/panTro4.reject.bed")
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
35 #elif str($tool_mode.reference) == "xenTro3":
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
36 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/xenTro3/xenTro3.accept.bed")
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
37 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/xenTro3/xenTro3.reject.bed")
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
38 #elif str($tool_mode.reference) == "celWS235":
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
39 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/celWS235/celWS235.accept.bed")
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
40 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/celWS235/celWS235.reject.bed")
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
41 #elif str($tool_mode.reference) == "tair10":
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
42 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/tair10/tair10.accept.bed")
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
43 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/tair10/tair10.reject.bed")
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
44 #end if
8
c1cc480c53da Uploaded
rnateam
parents: 6
diff changeset
45 BlockClustPipeLine.pl -m TEST -c \$BLOCKCLUST_DATA_PATH/blockclust.config
0
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
46 -t $tool_mode.input_bbo
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
47 -a #echo ''.join( $accept_bed )
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
48 -r #echo ''.join( $reject_bed )
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
49 -o $outputdir
8
c1cc480c53da Uploaded
rnateam
parents: 6
diff changeset
50 #if $tool_mode.nochr:
c1cc480c53da Uploaded
rnateam
parents: 6
diff changeset
51 -nochr
c1cc480c53da Uploaded
rnateam
parents: 6
diff changeset
52 #end if
0
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
53 #if str($tool_mode.pred.enable_pred) == "yes":
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
54 -p
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
55 -pm $tool_mode.pred.pred_mode
8
c1cc480c53da Uploaded
rnateam
parents: 6
diff changeset
56 -md \$BLOCKCLUST_DATA_PATH/models;
0
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
57 #if str($tool_mode.pred.pred_mode) == "nearest_neighbour":
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
58 cp #echo os.path.join($outputdir,'nearest_neighbour_predictions.txt')# $nearest_neighbour_pred_bed;
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
59 #elif str($tool_mode.pred.pred_mode) == "model_based":
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
60 cp #echo os.path.join($outputdir,'model_based_predictions.txt')# $model_based_pred_bed;
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
61 #end if
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
62 #else:
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
63 ;
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
64 #end if
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
65
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
66 cp #echo os.path.join($outputdir, 'mcl_clusters','all_clusters.bed')# $clusters;
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
67 cp #echo os.path.join($outputdir, 'hclust_tree.pdf')# $hclust_plot;
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
68 cp #echo os.path.join($outputdir, 'discretized.gspan.tab')# $sim_tab_out
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
69 #elif str($tool_mode.operation) == "post":
6
6721468f2f9f Uploaded
rnateam
parents: 4
diff changeset
70 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 ./;
0
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
71 #end if
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
72 </command>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
73 <inputs>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
74 <conditional name="tool_mode">
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
75 <param name="operation" type="select" label="Select mode of operation">
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
76 <option value="pre">Pre-processing </option>
2
f973ec6e5192 Uploaded
rnateam
parents: 1
diff changeset
77 <option value="clust">Clustering and classification</option>
0
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
78 <option value="post">Post-processing</option>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
79 </param>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
80 <when value="pre">
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
81 <param name="reads_bam" type="data" format="bam" label="BAM file containing alignments" />
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
82 </when>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
83 <when value="clust">
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
84 <param name="input_bbo" type="data" format="tabular" label="Input blockgroups file" />
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
85 <param name="reference" type="select" label="Select reference genome">
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
86 <option value="hg19">Human (hg19)</option>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
87 <option value="mm10">Mouse (mm10)</option>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
88 <option value="dm3">Fly (dm3)</option>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
89 <option value="rheMac3">Monkey (rheMac3)</option>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
90 <option value="panTro4">Chimp (panTro4)</option>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
91 <option value="xenTro3">Frog (xenTro3)</option>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
92 <option value="celWS235">C. elegans (celWS235)</option>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
93 <option value="tair10">Arabidopsis thaliana (tair10)</option>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
94 </param>
8
c1cc480c53da Uploaded
rnateam
parents: 6
diff changeset
95 <param name="nochr" type="boolean" label="My input files have no 'chr' for chromosome names" checked="False"/>
0
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
96 <conditional name="pred">
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
97 <param name="enable_pred" type="select" label="Would you like to perform classification?">
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
98 <option value="no">No</option>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
99 <option value="yes">Yes</option>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
100 </param>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
101 <when value="yes">
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
102 <param name="pred_mode" type="select" label="Mode of classification">
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
103 <option value="model_based">Model based</option>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
104 <option value="nearest_neighbour">Nearest neighbour</option>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
105 </param>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
106 </when>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
107 </conditional>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
108 </when>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
109 <when value="post">
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
110 <param name="cmsearch_out" type="data" format="tabular" label="Output of cmsearch tool" />
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
111 <param name="clusters_bed" type="data" format="bed" label="BED file containing clusters (output of BlockClust)" />
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
112 <param name="sim_tab_in" type="data" format="tabular" label="Pairwise similarities file" />
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
113 </when>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
114 </conditional>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
115 </inputs>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
116
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
117 <outputs>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
118 <data format="bed" name="tags_bed" label="BlockClust: BAM to BED on ${on_string}">
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
119 <filter> tool_mode["operation"]=="pre"</filter>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
120 </data>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
121 <data format="pdf" name="hclust_plot" label="BlockClust: Hierarchical clustering plot on ${on_string}" >
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
122 <filter> tool_mode["operation"]=="clust"</filter>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
123 </data>
2
f973ec6e5192 Uploaded
rnateam
parents: 1
diff changeset
124 <data format="bed" name="clusters" label="BlockClust: BED of predicted clusters on ${on_string}">
0
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
125 <filter> tool_mode["operation"]=="clust"</filter>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
126 </data>
2
f973ec6e5192 Uploaded
rnateam
parents: 1
diff changeset
127 <data format="bed" name="model_based_pred_bed" label="BlockClust: Model based predictions BED on ${on_string}">
0
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
128 <filter>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
129 ((
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
130 tool_mode["operation"] == 'clust' and
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
131 tool_mode["pred"]["enable_pred"] == "yes" and
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
132 tool_mode["pred"]["pred_mode"] == "model_based"
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
133 ))
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
134 </filter>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
135 </data>
2
f973ec6e5192 Uploaded
rnateam
parents: 1
diff changeset
136 <data format="bed" name="nearest_neighbour_pred_bed" label="BlockClust: Nearest neighbor predictions BED on ${on_string}">
0
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
137 <filter>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
138 ((
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
139 tool_mode["operation"] == 'clust' and
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
140 tool_mode["pred"]["enable_pred"] == "yes" and
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
141 tool_mode["pred"]["pred_mode"] == "nearest_neighbour"
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
142 ))
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
143 </filter>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
144 </data>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
145 <data format="tabular" name="sim_tab_out" label="BlockClust: Pairwise similarities on ${on_string}">
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
146 <filter> tool_mode["operation"]=="clust"</filter>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
147 </data>
1
a92d8689aa30 Uploaded
rnateam
parents: 0
diff changeset
148 <data format="pdf" name="cluster_dist" from_work_dir="cluster_distribution.pdf" label="BlockClust: Cluster distribution on ${on_string}" >
0
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
149 <filter> tool_mode["operation"]=="post"</filter>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
150 </data>
1
a92d8689aa30 Uploaded
rnateam
parents: 0
diff changeset
151 <data format="pdf" name="cluster_hclust" from_work_dir="hclust_tree_clusters.pdf" label="BlockClust: Hierarchical clustering plot of cluster centroids on ${on_string}" >
0
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
152 <filter> tool_mode["operation"]=="post"</filter>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
153 </data>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
154 </outputs>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
155 <help>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
156
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
157 .. class:: infomark
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
158
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
159 **What it does**
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
160
2
f973ec6e5192 Uploaded
rnateam
parents: 1
diff changeset
161 BlockClust is an efficient approach to detect transcripts with similar
f973ec6e5192 Uploaded
rnateam
parents: 1
diff changeset
162 processing patterns. We propose a novel way to encode expression profiles
f973ec6e5192 Uploaded
rnateam
parents: 1
diff changeset
163 in compact discrete structures, which can then be processed using
f973ec6e5192 Uploaded
rnateam
parents: 1
diff changeset
164 fast graph-kernel techniques. BlockClust allows both clustering and
f973ec6e5192 Uploaded
rnateam
parents: 1
diff changeset
165 classification of small non-coding RNAs.
f973ec6e5192 Uploaded
rnateam
parents: 1
diff changeset
166
4
49e600128a73 Uploaded
rnateam
parents: 3
diff changeset
167 BlockClust runs in three operating modes:
49e600128a73 Uploaded
rnateam
parents: 3
diff changeset
168
2
f973ec6e5192 Uploaded
rnateam
parents: 1
diff changeset
169 1) Pre-processing - converts given mapped reads (BAM) into BED file of tags
4
49e600128a73 Uploaded
rnateam
parents: 3
diff changeset
170
49e600128a73 Uploaded
rnateam
parents: 3
diff changeset
171 2) Clustering and classification - of given input blockgroups (output of blockbuster tool) as explained in the original paper.
49e600128a73 Uploaded
rnateam
parents: 3
diff changeset
172
6
6721468f2f9f Uploaded
rnateam
parents: 4
diff changeset
173 3) Post-processing - plots for overview of predicted clusters.
2
f973ec6e5192 Uploaded
rnateam
parents: 1
diff changeset
174
f973ec6e5192 Uploaded
rnateam
parents: 1
diff changeset
175 For a thorough analysis of your data, we suggest you to use complete blockclust workflow, which contains all three modes of operation.
0
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
176
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
177 **Inputs**
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
178
2
f973ec6e5192 Uploaded
rnateam
parents: 1
diff changeset
179 BlockClust input files are dependent on the mode of operation:
4
49e600128a73 Uploaded
rnateam
parents: 3
diff changeset
180
49e600128a73 Uploaded
rnateam
parents: 3
diff changeset
181 1. Pre-processing mode:
49e600128a73 Uploaded
rnateam
parents: 3
diff changeset
182 * Binary Sequence Alignment Map (BAM) file
2
f973ec6e5192 Uploaded
rnateam
parents: 1
diff changeset
183
4
49e600128a73 Uploaded
rnateam
parents: 3
diff changeset
184 2. Clustering and classification:
49e600128a73 Uploaded
rnateam
parents: 3
diff changeset
185 * A blockgroups file generated by blockbuster tool
49e600128a73 Uploaded
rnateam
parents: 3
diff changeset
186 * Select reference genome
2
f973ec6e5192 Uploaded
rnateam
parents: 1
diff changeset
187
4
49e600128a73 Uploaded
rnateam
parents: 3
diff changeset
188 3. Post-processing:
49e600128a73 Uploaded
rnateam
parents: 3
diff changeset
189 * Output of cmsearch, searched clusters generated by BlockClust against Rfam
49e600128a73 Uploaded
rnateam
parents: 3
diff changeset
190 * BED file containing clusters generated by BlockClust
49e600128a73 Uploaded
rnateam
parents: 3
diff changeset
191 * Pairwise similarities of blockgroups generated by BlockClust
0
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
192
4
49e600128a73 Uploaded
rnateam
parents: 3
diff changeset
193 **Outputs**
49e600128a73 Uploaded
rnateam
parents: 3
diff changeset
194
49e600128a73 Uploaded
rnateam
parents: 3
diff changeset
195 1. Pre-processing mode:
49e600128a73 Uploaded
rnateam
parents: 3
diff changeset
196 * BED file of tags with expressions
0
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
197
4
49e600128a73 Uploaded
rnateam
parents: 3
diff changeset
198 2. Clustering and classification:
49e600128a73 Uploaded
rnateam
parents: 3
diff changeset
199 * Hierarchical clustering plot of all input blockgroups by their similarity
49e600128a73 Uploaded
rnateam
parents: 3
diff changeset
200 * Pairwise similarities of all input blockgroups
49e600128a73 Uploaded
rnateam
parents: 3
diff changeset
201 * BED file containing predicted clusters
49e600128a73 Uploaded
rnateam
parents: 3
diff changeset
202 * BED file containing prediction of blockgroups by pre-compiled SVM binary classification model.
2
f973ec6e5192 Uploaded
rnateam
parents: 1
diff changeset
203
4
49e600128a73 Uploaded
rnateam
parents: 3
diff changeset
204 3. Post-processing:
6
6721468f2f9f Uploaded
rnateam
parents: 4
diff changeset
205 * 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.
4
49e600128a73 Uploaded
rnateam
parents: 3
diff changeset
206 * Hierarchical clustering made out of centroids of each BlockClust predicted cluster
0
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
207
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
208 ------
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
209
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
210 **References**
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
211
3
27dde42069e0 Uploaded
rnateam
parents: 2
diff changeset
212 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.
0
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
213
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
214
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
215 </help>
768a67f6ae18 Uploaded
rnateam
parents:
diff changeset
216 </tool>