Mercurial > repos > bgruening > deeptools_bam_compare
comparison bamCompare.xml @ 1:e237a134059a draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
author | bgruening |
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date | Mon, 15 Feb 2016 10:33:27 -0500 |
parents | 105b9da2445c |
children | 2f27bfe8b570 |
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194 </test> | 194 </test> |
195 </tests> | 195 </tests> |
196 <help> | 196 <help> |
197 <![CDATA[ | 197 <![CDATA[ |
198 | 198 |
199 **What it does** | 199 What it does |
200 | 200 ------------- |
201 This tool compares two BAM files based on the number of mapped reads. To | 201 |
202 compare the BAM files, the genome is partitioned into bins of equal size, then | 202 This tool can be used to generate a bigWig or bedGraph file based on **two BAM** files that are compared to each other while being simultaneously normalized for sequencing depth. |
203 the number of reads found in each BAM file is counted per bin and | 203 |
204 finally a summary value reported. This value can be the ratio of the | 204 To compare the BAM files to each other, the genome is partitioned into bins of equal size, then the number of reads found in each BAM file is counted per bin, and finally a summary value reported. |
205 number of reads per bin, the log2 of the ratio or the difference. This tool | 205 This value can be the ratio of the number of reads per bin, the log2 of the ratio, or the difference. |
206 can normalize the number of reads in each BAM file using the SES method | 206 |
207 proposed in Diaz et al. (2012). "Normalization, bias correction, and peak | 207 This tool can normalize the number of reads in each BAM file using the SES method proposed in Diaz et al. (2012). "Normalization, bias correction, and peak |
208 calling for ChIP-seq". Statistical applications in genetics and molecular | 208 calling for ChIP-seq". Statistical applications in genetics and molecular |
209 biology, 11(3). Normalization based on read counts is also available. The | 209 biology, 11(3). |
210 output is either a bedgraph or a bigwig file containing the bin location and | 210 |
211 the resulting comparison values. By default, if reads are mated, the fragment | 211 Normalization based on read counts is also available. |
212 length reported in the BAM file is used. In the case of paired-end mapping, | 212 |
213 each read mate is treated independently to avoid a bias when a mixture of | 213 By default, if reads are from a paired-end sequencing run and reads are properly paired, the fragment length reported in the BAM file is used. |
214 concordant and discordant pairs are present. This means that *each end* will be | 214 |
215 extended to match the fragment length. | 215 **Note:** *For paired-end sequencing samples, each read mate is treated independently to avoid a bias when a mixture of concordant and discordant pairs are present. This means that _each end_ will be extended to match the fragment length.* |
216 | |
217 | 216 |
218 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png | 217 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png |
219 | 218 :width: 600 |
220 | 219 :height: 336 |
221 You can find more details on the bamCompare doc page: https://deeptools.readthedocs.org/en/master/content/tools/bamCompare.html | 220 |
222 | 221 Output files |
223 | 222 -------------- |
224 **Output files**: | 223 |
225 | 224 ``bamCompare`` produces the same kind of output as ``bamCoverage``. |
226 - same as for bamCoverage, except that you now obtain 1 coverage file that is based on 2 BAM files. | 225 The difference is that you now obtain 1 coverage file that is based on 2 BAM files: a bedGraph or a bigwig file containing the bin location and the resulting comparison values. |
226 | |
227 Like BAM files, bigWig files are compressed, binary files. If you would like to see the coverage values, choose the bedGraph output. For more information on typical NGS file formats, see our `Glossary <http://deeptools.readthedocs.org/en/latest/content/help_glossary.html#file-formats>`_ | |
228 | |
229 .. image:: $PATH_TO_IMAGES/bamCompare_output.png | |
230 :width: 600 | |
231 :height: 436 | |
227 | 232 |
228 ----- | 233 ----- |
229 | 234 |
230 @REFERENCES@ | 235 @REFERENCES@ |
231 ]]> | 236 ]]> |