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comparison ideas.xml @ 88:462ce06410c6 draft

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author greg
date Thu, 24 Aug 2017 10:12:45 -0400
parents 665b0feae3de
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87:665b0feae3de 88:462ce06410c6
146 <param name="cell_type_epigenetic_factor" type="select" label="Set cell type and epigenetic factor names by"> 146 <param name="cell_type_epigenetic_factor" type="select" label="Set cell type and epigenetic factor names by">
147 <option value="extract" selected="true">extracting them from the selected input file names</option> 147 <option value="extract" selected="true">extracting them from the selected input file names</option>
148 <option value="manual">manually setting them for each selected input</option> 148 <option value="manual">manually setting them for each selected input</option>
149 </param> 149 </param>
150 <when value="extract"> 150 <when value="extract">
151 <param name="input" type="data" format="bigwig,bam" multiple="True" label="BAM or BigWig file"> 151 <param name="input" type="data" format="bigwig,bam" multiple="True" label="BAM or BigWig files">
152 <validator type="empty_field"/> 152 <validator type="empty_field"/>
153 <validator type="unspecified_build"/> 153 <validator type="unspecified_build"/>
154 </param> 154 </param>
155 <param name="input_name_positions" type="select" display="radio" label="Selected input file name pattern is" help="A '-' character must separate cell type and epigenetic factor names within the selected input file names"> 155 <param name="input_name_positions" type="select" display="radio" label="Selected input file name pattern is" help="A '-' character must separate cell type and epigenetic factor names within the selected input file names">
156 <option value="cell_first" selected="true">Cell type name - Epigenetic factor name</option> 156 <option value="cell_first" selected="true">Cell type name - Epigenetic factor name</option>
237 identify the best model size fitting to the data so users do not have to specify the number of states. On the other hand, users can 237 identify the best model size fitting to the data so users do not have to specify the number of states. On the other hand, users can
238 still specify the number of states if desired. 238 still specify the number of states if desired.
239 239
240 ----- 240 -----
241 241
242 **Required options** 242 **Options**
243 243
244 * **Cell type, Epigenetic factor and Input** - specify any number of inputs with currently supported formats, either bam or bigwig. The cell name + factor name must be unique for each input. For example, if you have replicate data you may want to specify the cell name as "cell_rep1", "cell_rep2", etc and the factor name as "factor_rep1", "factor_rep2", etc. 244 * **Select input type** - select a data matrix file produced in a previous run or one or more Bam or Bigwig datasets.
245 * **Set cell type and epigenetic factor names by** - cell type and epigenetic factor names can be set manually or by extracting them from the names of the selected input datasets. The latter case requires all selected datasets to have names that contain a "-" character.
246
247 * **BAM or BigWig files** - select one or more Bam or Bigwig files from yhour history, making sure that the name of every selected input include a "-" character.
248 * **Cell type, Epigenetic factor and Input** - manually select any number of inputs, setting the cell type and epigenetic factor name for each. The combination of "cell type name" and "epigenetic factor name" must be unique for each input. For example, if you have replicate data you may want to specify the cell name as "cell_rep1", "cell_rep2", etc and the factor name as "factor_rep1", "factor_rep2", etc.
245 249
246 * **Cell type name** - cell type name 250 * **Cell type name** - cell type name
247 * **Epigenetic factor name** - epigenetic factor name 251 * **Epigenetic factor name** - epigenetic factor name
248 * **BAM or BigWig file** - BAM or BigWig file 252 * **BAM or BigWig file** - BAM or BigWig file
249 253
250 * **Set genomic windows on which to process the data** - if "No" is selected, IDEAS will run whole genome segmentation. If "Yes" is selected, IDEAS will segment genomes in the unit of the windows defined by the bed file. This file can be in BED3, BED4 or BED5 format, but only the first three columns (chr posst posed) will be used. 254 * **Select Bed file that defines genomic windows on which to process the data** - if "No" is selected, IDEAS will run whole genome segmentation. If "Yes" is selected, IDEAS will segment genomes in the unit of the windows defined by the bed file. This file can be in BED3, BED4 or BED5 format, but only the first three columns (chr posst posed) will be used.
251 255
252 * **Window size in base pairs** - Window size in base pairs (if "No" is selected) 256 * **Window size in base pairs** - Window size in base pairs (if "No" is selected)
253 * **Restrict processing to specified chromosomes** - If "Yes" is selected, processing will be restricted to specified chromosomes 257 * **Restrict processing to specified chromosomes** - If "Yes" is selected, processing will be restricted to specified chromosomes
254 258
255 * **Chromosomes** - processing will be restricted to specified chromosomes (if "Yes" is selected) 259 * **Chromosomes** - processing will be restricted to specified chromosomes (if "Yes" is selected)
256 260
257 * **Chromosome** - specified chromosome 261 * **Bed file specifying the genomic windows** - bed file specifying the genomic windows (if "Yes" is selected)
258
259 * **Bed file specifying the genomic windows** - bed file specifying the genomic windows (if "Yes" is selected)
260
261 **Other options**
262 262
263 * **Output chromosomes in separate files** - select "Yes" to produce separate files for each chromosome, allowing you to run IDEAS on different chromosomes separately. 263 * **Output chromosomes in separate files** - select "Yes" to produce separate files for each chromosome, allowing you to run IDEAS on different chromosomes separately.
264 * **Calculate the average signal in each genomic window using** - use the bigWigAverageOverBed utility from the UCSC genome browser to calculate average signal (number of reads per bp) in each genomic window. 264 * **Calculate the average signal in each genomic window using** - use the bigWigAverageOverBed utility from the UCSC genome browser to calculate average signal (number of reads per bp) in each genomic window.
265 * **Select file(s) containing regions to exclude** - select one or more bed files that contains regions you'd like excluded from your datasets. 265 * **Select file(s) containing regions to exclude** - select one or more bed files that contains regions you'd like excluded from your datasets.
266 * **Standardize all datasets** - select "Yes" to standardize all datasets (e.g., reads / total_reads * 20 million) so that the signals from different cell types become comparable - your datasets can be read counts, logp-values or fold change. 266 * **Standardize all datasets** - select "Yes" to standardize all datasets (e.g., reads / total_reads * 20 million) so that the signals from different cell types become comparable - your datasets can be read counts, logp-values or fold change.
269 * **Use log2(x+number) transformation** - perform Log2-transformation of the input data by log2(x+number) (recommended for read count data to reduce skewness). You can enter a number less than 1. For example, if your input data is mean read count per window, using 0.1 may produce better results. 269 * **Use log2(x+number) transformation** - perform Log2-transformation of the input data by log2(x+number) (recommended for read count data to reduce skewness). You can enter a number less than 1. For example, if your input data is mean read count per window, using 0.1 may produce better results.
270 * **Maximum number of states to be inferred** - restrict the maximum number of states to be generated by IDEAS; the final number of inferred states may be smaller than the number you specified 270 * **Maximum number of states to be inferred** - restrict the maximum number of states to be generated by IDEAS; the final number of inferred states may be smaller than the number you specified
271 * **Initial number of states** - while IDEAS may infer 30 states or more by starting from just 20 states, it may not do so if it is trapped in a local mode. We recommend setting the initial number of states slightly larger than the number of states you expect. 271 * **Initial number of states** - while IDEAS may infer 30 states or more by starting from just 20 states, it may not do so if it is trapped in a local mode. We recommend setting the initial number of states slightly larger than the number of states you expect.
272 * **Maximum number of position classes to be inferred** - Set this value only if: 272 * **Maximum number of position classes to be inferred** - Set this value only if:
273 273
274 * you do not want position classes (e.g., for testing purposes), in this case set the value to 1 274 * you do not want position classes (e.g., for testing purposes), in this case set the value to 1
275 * IDEAS runs slow because there are too many position classes, generally less than 100 position classes will run fine 275 * IDEAS runs slow because there are too many position classes, generally less than 100 position classes will run fine
276 276
277 * **Maximum number of cell type clusters allowed** - Set this value only for testing. If you set the value to 1, then all cell types will be clustered in one group. 277 * **Maximum number of cell type clusters allowed** - Set this value only for testing. If you set the value to 1, then all cell types will be clustered in one group.
278 * **Prior concentration** - specify the prior concentration parameter; default is A=sqrt(number of cell types). A smaller concentration parameter (e.g., 1 or less) will emphasize more on position specificity and a larger concentration parameter (e.g., 10 * number of cell types) will emphasize more on global homogeneity. 278 * **Prior concentration** - specify the prior concentration parameter; default is A=sqrt(number of cell types). A smaller concentration parameter (e.g., 1 or less) will emphasize more on position specificity and a larger concentration parameter (e.g., 10 * number of cell types) will emphasize more on global homogeneity.
279 * **Set the the number of burnin and maximization steps** - specify the number of burnin and maximization steps; default it is 50 50. Increasing these two numbers will increase computing and only slightly increase accuracy. Decreasing these two numbers will reduce computing but may also reduce accuracy. We recommend to run IDEAS with at least 20 burnins and 20 maximizations. IDEAS will not stop even if it reaches a maximum mode. 279 * **Set the the number of burnin and maximization steps** - specify the number of burnin and maximization steps; default it is 50 50. Increasing these two numbers will increase computing and only slightly increase accuracy. Decreasing these two numbers will reduce computing but may also reduce accuracy. We recommend to run IDEAS with at least 20 burnins and 20 maximizations. IDEAS will not stop even if it reaches a maximum mode.
280 * **Minimum standard deviation for the emission Gaussian distribution** - you should change the default value of 0.5 if the standard deviation of your data is much smaller or much larger than 1. The first line of the output produced by IDEAS is **ysd=xxx**, which is the total standard deviation of your data. If that value is less than 0.5, you may set the minimum standard deviation to an even smaller number (e.g., xxx/2). If the standard deviation of your data is much greater than 1, (e.g., 20), you may set the minimum standard deviation to a larger value, (e.g., 5). Modifying the minimum standard deviation in the former case is more necessary than in the latter case because otherwise you may end up finding no interesting segmentations. We do not recommend setting the minimum standard deviation to be 0 or smaller, as doing so may capture some artificial and uninteresting states due to tightly clustered data, such as 0 in read counts. 280 * **Minimum standard deviation for the emission Gaussian distribution** - you should change the default value of 0.5 if the standard deviation of your data is much smaller or much larger than 1. The first line of the output produced by IDEAS is **ysd=xxx**, which is the total standard deviation of your data. If that value is less than 0.5, you may set the minimum standard deviation to an even smaller number (e.g., xxx/2). If the standard deviation of your data is much greater than 1, (e.g., 20), you may set the minimum standard deviation to a larger value, (e.g., 5). Modifying the minimum standard deviation in the former case is more necessary than in the latter case because otherwise you may end up finding no interesting segmentations. We do not recommend setting the minimum standard deviation to be 0 or smaller, as doing so may capture some artificial and uninteresting states due to tightly clustered data, such as 0 in read counts.