Mercurial > repos > joachim-jacob > qualimap_suite

comparison bamqc.xml @ 3:9537dd9dd18b draft

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author joachim-jacob
date Tue, 12 Feb 2013 04:50:47 -0500
parents 934cd08c77af
children 3d690162d629
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2:934cd08c77af 3:9537dd9dd18b
67 #end if 67 #end if
68 </configfile> 68 </configfile>
69 </configfiles> 69 </configfiles>
70 70
71 <tests> 71 <tests>
72 <!-- Test base-space single-end reads with pre-built index and preset parameters -->
73 <test>
74 <!-- TopHat commands:
75 tophat -o tmp_dir -p 1 tophat_in1 test-data/tophat_in2.fastqsanger
76 Rename the files in tmp_dir appropriately
77 -->
78 <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger" />
79 <param name="genomeSource" value="indexed" />
80 <param name="index" value="tophat_test" />
81 <param name="sPaired" value="single" />
82 <param name="sSettingsType" value="preSet" />
83 <output name="junctions" file="tophat_out1j.bed" />
84 <output name="accepted_hits" file="tophat_out1h.bam" compare="sim_size" />
85 </test>
86 <!-- Test using base-space test data: paired-end reads, index from history. -->
87 <test>
88 <!-- TopHat commands:
89 bowtie-build -f test-data/tophat_in1.fasta tophat_in1
90 tophat -o tmp_dir -p 1 -r 20 tophat_in1 test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger
91 Rename the files in tmp_dir appropriately
92 -->
93 <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger" />
94 <param name="genomeSource" value="history" />
95 <param name="ownFile" ftype="fasta" value="tophat_in1.fasta" />
96 <param name="sPaired" value="paired" />
97 <param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger" />
98 <param name="mate_inner_distance" value="20" />
99 <param name="pSettingsType" value="preSet" />
100 <output name="junctions" file="tophat_out2j.bed" />
101 <output name="accepted_hits" file="tophat_out2h.bam" compare="sim_size" />
102 </test>
103 <!-- Test base-space single-end reads with user-supplied reference fasta and full parameters -->
104 <test>
105 <!-- Tophat commands:
106 bowtie-build -f test-data/tophat_in1.fasta tophat_in1
107 tophat -o tmp_dir -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +closure-search +min-closure-exon 50 +min-closure-intron 50 +max-closure-intro 5000 +microexon-search tophat_in1 test-data/tophat_in2.fastqsanger
108 Replace the + with double-dash
109 Rename the files in tmp_dir appropriately
110 -->
111 <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger"/>
112 <param name="genomeSource" value="history"/>
113 <param name="ownFile" value="tophat_in1.fasta"/>
114 <param name="sPaired" value="single"/>
115 <param name="sSettingsType" value="full"/>
116 <param name="library_type" value="FR Unstranded"/>
117 <param name="anchor_length" value="8"/>
118 <param name="splice_mismatches" value="0"/>
119 <param name="min_intron_length" value="70"/>
120 <param name="max_intron_length" value="500000"/>
121 <param name="max_multihits" value="40"/>
122 <param name="min_segment_intron" value="50" />
123 <param name="max_segment_intron" value="500000" />
124 <param name="seg_mismatches" value="2"/>
125 <param name="seg_length" value="25"/>
126 <param name="allow_indel_search" value="Yes"/>
127 <param name="max_insertion_length" value="3"/>
128 <param name="max_deletion_length" value="3"/>
129 <param name="use_junctions" value="Yes" />
130 <param name="use_annotations" value="No" />
131 <param name="use_juncs" value="No" />
132 <param name="no_novel_juncs" value="No" />
133 <param name="use_search" value="Yes" />
134 <param name="min_closure_exon" value="50" />
135 <param name="min_closure_intron" value="50" />
136 <param name="max_closure_intron" value="5000" />
137 <param name="use_search" value="Yes" />
138 <param name="min_coverage_intron" value="50" />
139 <param name="max_coverage_intron" value="20000" />
140 <param name="microexon_search" value="Yes" />
141 <output name="insertions" file="tophat_out3i.bed" />
142 <output name="deletions" file="tophat_out3d.bed" />
143 <output name="junctions" file="tophat_out3j.bed" />
144 <output name="accepted_hits" file="tophat_out3h.bam" compare="sim_size" />
145 </test>
146 <!-- Test base-space paired-end reads with user-supplied reference fasta and full parameters -->
147 <test>
148 <!-- TopHat commands:
149 tophat -o tmp_dir -r 20 -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +microexon-search tophat_in1 test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger
150 Replace the + with double-dash
151 Rename the files in tmp_dir appropriately
152 -->
153 <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger"/>
154 <param name="genomeSource" value="indexed"/>
155 <param name="index" value="tophat_test"/>
156 <param name="sPaired" value="paired"/>
157 <param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger"/>
158 <param name="mate_inner_distance" value="20"/>
159 <param name="pSettingsType" value="full"/>
160 <param name="library_type" value="FR Unstranded"/>
161 <param name="mate_std_dev" value="20"/>
162 <param name="anchor_length" value="8"/>
163 <param name="splice_mismatches" value="0"/>
164 <param name="min_intron_length" value="70"/>
165 <param name="max_intron_length" value="500000"/>
166 <param name="max_multihits" value="40"/>
167 <param name="min_segment_intron" value="50" />
168 <param name="max_segment_intron" value="500000" />
169 <param name="seg_mismatches" value="2"/>
170 <param name="seg_length" value="25"/>
171 <param name="allow_indel_search" value="No"/>
172 <param name="use_junctions" value="Yes" />
173 <param name="use_annotations" value="No" />
174 <param name="use_juncs" value="No" />
175 <param name="no_novel_juncs" value="No" />
176 <param name="use_search" value="No" />
177 <param name="microexon_search" value="Yes" />
178 <output name="junctions" file="tophat_out4j.bed" />
179 <output name="accepted_hits" file="tophat_out4h.bam" compare="sim_size" />
180 </test>
181 </tests> 72 </tests>
182 73
183 <help> 74 <help>
184 **Tool Overview** 75 **Tool Overview**
185 76
186 Tool_ allows for simply but throroughly checking of the quality of mapping. 77 Bamqc_ allows for simply but throroughly checking of the quality of mapping.
187 78
188 .. _Tool: http://qualimap.bioinfo.cipf.es// 79 .. _Bamqc: http://qualimap.bioinfo.cipf.es//
189 80
190 ------ 81 ------
191
192 **Know what you are doing**
193
194 .. class:: warningmark
195
196 Know what you are doing by reading the `documentation`__ and experimenting.
197
198 .. __: http://tophat.cbcb.umd.edu/manual.html
199
200 ------
201
202 **Input formats**
203
204 Tool accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files.
205
206 ------
207
208 **Outputs**
209
210 Tool produces two output files:
211
212 - junctions -- A UCSC BED_ track of junctions reported by TopHat. Each junction consists of two connected BED blocks, where each block is as long as the maximal overhang of any read spanning the junction. The score is the number of alignments spanning the junction.
213 - accepted_hits -- A list of read alignments in BAM_ format.
214
215 .. _BED: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
216 .. _BAM: http://samtools.sourceforge.net/
217
218 Two other possible outputs, depending on the options you choose, are insertions and deletions, both of which are in BED format.
219
220 -------
221
222 **Tool settings**
223
224 All of the options have a default value. You can change any of them. Some of the options in Tophat have been implemented here.
225
226 ------
227
228 **Tool parameter list**
229
230 This is a list of implemented Tophat options::
231
232 -r This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments
233 selected at 300bp, where each end is 50bp, you should set -r to be 200. There is no default, and this parameter
234 is required for paired end runs.
235 82
236 </help> 83 </help>
237 </tool> 84 </tool>
238 85