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1 **Fully automated pipeline for detection of sex linked genes using RNA-Seq data**
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3 This pipeline has been designed for detection of sex-linked genes from the cross using RNASeq data.
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4 It contains two workflows, one for detection of Y-linked and one for detection of X-linked genes.
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6 INSTALLING PREREQUISITES
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7 You will need 3 prerequisites in order to successfully run this pipeline:
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8 1) install linkyx
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9 2) install tool dependencies
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10 3) import workflows
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12 1) The easiest way how to install linkyx tools is to login to your local Galaxy instance and click
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13 Admin -> Search and browse tool sheds -> Galaxy main tool shed -> linkyx
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14
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15 Click on the tool and then simply press button "Install to Galaxy" in the upper part of the screen.
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16 This tool repository contains four tools:
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17 LINKYX_X
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18 Identify X linked contigs from cross
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20 LINKYX_Y
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21 Identify Y linked contigs from cross
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23 LINKYX_mpileup
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24 Run mpileup with LINKYX-specific parameters
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26 Reformat Trinity header
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28 All tools can be run independently, but the easiest way to obtain proper input files is via provided workflows.
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30 2) The dependencies can be installed in a similar fashion as linkyx tool from the Galaxy tool shed by searching
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31 for suite_linkyx_1_0
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33 3) When installing linkyx from toolshed, you can click on the "Workflows" on the main page describing the tool
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34 in the section "Contents of this repository". After clicking on either linkY or linkX, you will be presented an
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35 option to install the workflows by clicking "Install to Galaxy" button.
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37 RUNNING THE WORKFLOWS
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38 After you imported workflows to the galaxy and installed linkyx and workflow dependencies, the pipeline is ready to go.
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40 You can access it by clicking on the "Workflow" in the upper gray layer of your Galaxy instance. After clicking on the
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41 name of the workflow and choosing "Run", you will be requested to select input datasets, two for each member of the cross
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42 since paired-end reads are expected by default. If you don't have your data yet, test files are available in this repository.
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43 The computation for these files ends in ~5 minutes and outputs one X-linked and one Y-linked contig.
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45 CONTACT INFORMATION
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46 If you have any questions, please use following email address: biomonika@psu.edu |
