LoadGenome: Difference between revisions
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The LoadGenome page lets you add your own genome for use with CoGe's various tools. | The LoadGenome page lets you add your own genome for use with CoGe's various tools. Once your genome is loaded, you can add [[LoadAnnotation|annotation]] and [[LoadExperiment|experiment]] data. | ||
===Important Information=== | === Important Information === | ||
===Quick Start=== | *You must be logged into CoGe to use LoadGenome. | ||
# | *Your genome will be automatically assigned to your user account. | ||
#Version: what version is your genome (please use numbers) | *You can [[User#How_to_share_data|share]] your genome with other CoGe users or the public (only you can see it by default) | ||
*Please see CoGe's [[Data policy]] | |||
# Type: | |||
# Source: Where did you get your data? | === Quick Start === | ||
#'''Organism:''' select an organism for your genome. If your organism does not exist, please create it by clicking '''New'''. | |||
# Restricted: | #'''Version:''' what version is your genome (please use numbers). Example: 0.01 | ||
## If this is selected, only you have access to the data after it is loaded. | #'''Type:''' What kind of sequence is it (most are unmasked) | ||
## If this is not selected, your data is fully public. | #'''Source:''' Where did you get your data? This could be you, your lab, your university, a sequencing center, your collaborator. Please give credit and provide a link to the source. | ||
## Note: you can change this at any point (make it public, make it private, restrict who has access | #'''Restricted:''' | ||
# Add data files: | ##If this is selected, only you have access to the data after it is loaded. | ||
## iPlant Data Store: | ##If this is not selected, your data is fully public. | ||
## FTP/HTTP: May be slow, but useful if the data is already posted somewhere. | ##Note: you can change this at any point (make it public, make it private, restrict who has access | ||
#'''Add data files:''' You can specify multiple fasta data files for your genome | |||
##NCBI: specify genbank accessions for a genome. | ##iPlant Data Store: Fast, fast, fast. Also you can transfer data files that are larger than 2GB. See below for more info. | ||
##FTP/HTTP: May be slow, but useful if the data is already posted somewhere. Note that HTTP usually doesn't work for files greater than 2GB | |||
##Upload: upload from your computer. | ##NCBI: specify genbank accessions for a genome. Note: genomes retrieved from NCBI are made fully public | ||
##Upload: upload from your computer. Note: Doesn't usually work for files larger than 2GB | |||
#Press "Load Genome" when everything is ready! | #Press "Load Genome" when everything is ready! | ||
=== iPlant Data Store === | === iPlant Data Store === | ||
We prefer to use iPlant's Data Store to transfer your data to CoGe because it is easy to use (like dropbox), has a lot of free storage for scientists, and is very fast. | We prefer to use iPlant's Data Store to transfer your data to CoGe because it is easy to use (like dropbox), has a lot of free storage for scientists, and is very fast. There are two ways to access the Data Store from CoGe. | ||
====Quick-share link==== | #Quick-share link | ||
Data can be imported into CoGe using a Data Store quick-share link. | #The coge_data/ folder | ||
==== Quick-share link ==== | |||
Data can be imported into CoGe using a Data Store quick-share link. Follow the instructions below to generate a quick-share link, then paste the link into the URL field under "FTP/HTTP" data source in LoadGenome. | |||
#Upload Fasta and GFF (if available) files to iPlant Data Store | #Upload Fasta and GFF (if available) files to iPlant Data Store | ||
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##<youtube>CoHjYWSvrPA</youtube> | ##<youtube>CoHjYWSvrPA</youtube> | ||
====The coge_data/ folder==== | ==== The coge_data/ folder ==== | ||
CoGe has default access to any files in the folder named coge_data/ in your Data Store. | |||
CoGe has default access to any files in the folder named coge_data/ in your Data Store. Simple place your data files into that directory using iCommands or the Discovery Environment, then select the files under "Data Store" in LoadGenome. |
Revision as of 19:04, 2 April 2013
The LoadGenome page lets you add your own genome for use with CoGe's various tools. Once your genome is loaded, you can add annotation and experiment data.
Important Information
- You must be logged into CoGe to use LoadGenome.
- Your genome will be automatically assigned to your user account.
- You can share your genome with other CoGe users or the public (only you can see it by default)
- Please see CoGe's Data policy
Quick Start
- Organism: select an organism for your genome. If your organism does not exist, please create it by clicking New.
- Version: what version is your genome (please use numbers). Example: 0.01
- Type: What kind of sequence is it (most are unmasked)
- Source: Where did you get your data? This could be you, your lab, your university, a sequencing center, your collaborator. Please give credit and provide a link to the source.
- Restricted:
- If this is selected, only you have access to the data after it is loaded.
- If this is not selected, your data is fully public.
- Note: you can change this at any point (make it public, make it private, restrict who has access
- Add data files: You can specify multiple fasta data files for your genome
- iPlant Data Store: Fast, fast, fast. Also you can transfer data files that are larger than 2GB. See below for more info.
- FTP/HTTP: May be slow, but useful if the data is already posted somewhere. Note that HTTP usually doesn't work for files greater than 2GB
- NCBI: specify genbank accessions for a genome. Note: genomes retrieved from NCBI are made fully public
- Upload: upload from your computer. Note: Doesn't usually work for files larger than 2GB
- Press "Load Genome" when everything is ready!
iPlant Data Store
We prefer to use iPlant's Data Store to transfer your data to CoGe because it is easy to use (like dropbox), has a lot of free storage for scientists, and is very fast. There are two ways to access the Data Store from CoGe.
- Quick-share link
- The coge_data/ folder
Data can be imported into CoGe using a Data Store quick-share link. Follow the instructions below to generate a quick-share link, then paste the link into the URL field under "FTP/HTTP" data source in LoadGenome.
- Upload Fasta and GFF (if available) files to iPlant Data Store
- Quick Start Guide: https://pods.iplantcollaborative.org/wiki/display/start/Data+Store+Quick+Start
- Use Davis to generate a quick-share link to let others download the data
The coge_data/ folder
CoGe has default access to any files in the folder named coge_data/ in your Data Store. Simple place your data files into that directory using iCommands or the Discovery Environment, then select the files under "Data Store" in LoadGenome.