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comparison ALFA/alfa_wrapper.xml @ 24:887c6cb328e9 draft

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author charles-bernard
date Thu, 27 Oct 2016 10:49:16 -0400
parents 1714165f5df0
children 37fce32b0298
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23:c7279df3f7ba 24:887c6cb328e9
266 | Generation of indexes from an annotation file might be time consuming (i.e ~10min for the human genome). Thus, ALFA allows the user to submit directly indexes generated in previous runs. 266 | Generation of indexes from an annotation file might be time consuming (i.e ~10min for the human genome). Thus, ALFA allows the user to submit directly indexes generated in previous runs.
267 | 267 |
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269 .. class:: infomark 269 .. class:: infomark
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271 | ALFA also allows to use built-in indexes to save even more computational time. In order to generate these built-in indexes, install the data manager tool 'data_manager_build_alfa_indexes' available on the toolshed. 271 | ALFA also allows to use built-in indexes to save even more computational time. In order to generate easily these built-in indexes, install the data manager tool `data_manager_build_alfa_indexes`_ available on the toolshed.
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273 .. _data_manager_build_alfa_indexes: https://toolshed.g2.bx.psu.edu/view/charles-bernard/data_manager_build_alfa_indexes
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273 * **Input 2: Reads** 275 * **Input 2: Reads**
274 276
275 | ALFA requires as second input a single or a set of mapped reads file(s) in either bam or bedgraph format. The coordinates of the mapped reads will be intersected with the according categories and biotypes mentioned in the indexes. 277 | ALFA requires as second input a single or a set of mapped reads file(s) in either bam or bedgraph format. The coordinates of the mapped reads will be intersected with the according categories and biotypes mentioned in the indexes.
276 | The strandness option determines which strand of the annotated sequence will be taken into account during this intersection. 278 | The strandness option determines which strand of the annotated sequence will be taken into account during this intersection.