comparison README.txt @ 5:939e59027486

edited README
author biomonika <biomonika@psu.edu>
date Fri, 20 Feb 2015 14:55:29 -0500
parents 0979980b5bdc
children 3941ba0da626
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1 **Fully automated pipeline for detection of sex linked genes using RNA-Seq data** 1 **Fully automated pipeline for detection of sex linked genes using RNA-Seq data**
2 2
3 This pipeline has been designed for detection of sex-linked genes from the cross using RNASeq data. It contains two workflows, one for detection of Y-linked and one for detection of X-linked genes. 3 This pipeline has been designed for detection of sex-linked genes from the cross using RNASeq data.
4 It contains two workflows, one for detection of Y-linked and one for detection of X-linked genes.
4 5
5 INSTALLING PREREQUISITES 6 INSTALLING PREREQUISITES
6 You will need 3 prerequisites in order to successfully run this pipeline: 7 You will need 3 prerequisites in order to successfully run this pipeline:
7 1) install linkyx 8 1) install linkyx
8 2) install tool dependencies 9 2) install tool dependencies
9 3) import workflows 10 3) import workflows
10 11
11 1) The easiest way how to install linkyx tools is to login to your local Galaxy instance and click Admin -> Search and browse tool sheds -> Galaxy tool shed -> linkyx 12 1) The easiest way how to install linkyx tools is to login to your local Galaxy instance and click
13 Admin -> Search and browse tool sheds -> Galaxy tool shed -> linkyx
12 14
13 Click on the tool and then simply press button "Install to Galaxy" in the upper part of the screen. 15 Click on the tool and then simply press button "Install to Galaxy" in the upper part of the screen.
14 This tool repository contains four tools: 16 This tool repository contains four tools:
15 LINKYX_X 17 LINKYX_X
16 Identify X linked contigs from cross 18 Identify X linked contigs from cross
23 25
24 Reformat Trinity header 26 Reformat Trinity header
25 27
26 All tools can be run independently, but the easiest way to obtain proper input files is via provided workflows. 28 All tools can be run independently, but the easiest way to obtain proper input files is via provided workflows.
27 29
28 2) The dependencies can be installed in a similar fashion as linkyx tool from the Galaxy tool shed by searching for suite_linkyx_1_0 30 2) The dependencies can be installed in a similar fashion as linkyx tool from the Galaxy tool shed by searching
31 for suite_linkyx_1_0
29 32
30 3) When installing linkyx from toolshed, you can click on the "Workflows" on the main page describing the tool in the section "Contents of this repository". After clicking on either linkY or linkX, you will be presented an option to install the workflows by clicking "Install to Galaxy" button 33 3) When installing linkyx from toolshed, you can click on the "Workflows" on the main page describing the tool
34 in the section "Contents of this repository". After clicking on either linkY or linkX, you will be presented an
35 option to install the workflows by clicking "Install to Galaxy" button.
31 36
32 RUNNING THE WORKFLOWS 37 RUNNING THE WORKFLOWS
33 After you imported workflows to the galaxy and installed linkyx and workflow dependencies, the pipeline is ready to go. 38 After you imported workflows to the galaxy and installed linkyx and workflow dependencies, the pipeline is ready to go.
34 39
35 You can access it by clicking on the "Workflow" in the upper gray layer of your Galaxy instance. After clicking on the name of the workflow and choosing "Run", you will be requested to select input datasets, two for each member of the cross since paired-end reads are expected by default. If you don't have your data yet, test files are available in this repository. The computation for these files ends in ~5 minutes and outputs one X-linked and one Y-linked contig. 40 You can access it by clicking on the "Workflow" in the upper gray layer of your Galaxy instance. After clicking on the
41 name of the workflow and choosing "Run", you will be requested to select input datasets, two for each member of the cross
42 since paired-end reads are expected by default. If you don't have your data yet, test files are available in this repository.
43 The computation for these files ends in ~5 minutes and outputs one X-linked and one Y-linked contig.
36 44
37 CONTACT INFORMATION 45 CONTACT INFORMATION
38 If you have any questions, please use following email address: biomonika@psu.edu 46 If you have any questions, please use following email address: biomonika@psu.edu