Mercurial > repos > bgruening > deeptools
comparison correctGCBias.xml @ 5:1f312af2f8db draft
Uploaded
| author | bgruening |
|---|---|
| date | Tue, 06 Aug 2013 08:20:47 -0400 |
| parents | 21d563d5f2b2 |
| children | c5847db0cb41 |
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| 4:c8a0dc481493 | 5:1f312af2f8db |
|---|---|
| 1 <tool id="correctGCBias" name="correctGCBias" version="1.0.1"> | 1 <tool id="correctGCBias" name="correctGCBias" version="1.0.1"> |
| 2 <description> | 2 <description>use the output from computeGCBias to obtain corrected sample files</description> |
| 3 </description> | |
| 4 <requirements> | 3 <requirements> |
| 5 <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement> | 4 <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement> |
| 6 <requirement type="package" version="0.1">ucsc_tools</requirement> | 5 <requirement type="package" version="0.1">ucsc_tools</requirement> |
| 7 </requirements> | 6 </requirements> |
| 8 <command> | 7 <command> |
| 104 </outputs> | 103 </outputs> |
| 105 <help> | 104 <help> |
| 106 | 105 |
| 107 **What it does** | 106 **What it does** |
| 108 | 107 |
| 109 Computes the GC bias ussing Benjamini's method [citation]. The resulting GC | 108 This tool requires the output from computeGCBias to correct the given BAM files according to the method proposed by Benjamini and Speed (2012). Nucleic Acids Res. |
| 110 bias can later be used to plot the bias or to correct the bias. | 109 The resulting BAM files can be used in any downstream analyses, but be aware that you should not filter out duplicates from here on. |
| 111 | |
| 112 ----- | 110 ----- |
| 113 | 111 |
| 114 .. class:: infomark | 112 .. class:: infomark |
| 115 | 113 |
| 116 Please acknowledge that this tool **is still in development** and we will be very happy to receive feedback from the users. If you run into any trouble please sent an email to `Fidel Ramirez`_. | 114 If you would like to give us feedback or you run into any trouble, please sent an email to deeptools@googlegroups.com |
| 117 | 115 |
| 118 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. | 116 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. |
| 119 | 117 |
| 120 | 118 |
| 121 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/ | 119 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/ |