Mercurial > repos > charles-bernard > alfa

comparison ALFA/alfa_wrapper.xml @ 27:c3f91012ac19 draft

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author charles-bernard
date Fri, 04 Nov 2016 06:11:49 -0400
parents 37fce32b0298
children c8acc8808b52
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26:f1a20d50c495 27:c3f91012ac19
260 | Gtf File must be sorted. 260 | Gtf File must be sorted.
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265 | 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. 265 | 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 as inputs for a new run.
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270 | 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. 270 | 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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290 * **Output files** 290 * **Output files**
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292 | The result of the intersection is a count file displaying the count of nucleotides in the reads for each genomic categories and biotypes. From this count file, plots of the raw and normalized distributions of the reads among these categories are generated. 292 | The result of the intersection is a count file displaying the count of nucleotides in the reads for each genomic categories and biotypes. From this count file, plots of the raw and normalized distributions of the reads among these categories are generated.
293 | In the output files section, the user can choose what kind of files he desires as ALFA output. Categories Count File and Plots are proposed by default. 293 | In the output files section, the user can choose what kind of files he/she desires as ALFA output. Categories Count File and Plots are proposed by default.
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298 | The user can also select the 'indexes' option as output. This option is interesting if you plan to run ALFA again with the same submitted annotation file. *See Nota Bene/Input 1: Annotation File for more information.* 298 | The user can also select the 'indexes' option as output. This option is interesting if you plan to run ALFA again with the same submitted annotation file. *See Nota Bene/Input 1: Annotation File for more information.*