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For many genomes supported by UCSC, the refGene data collection from UCSC represent the canonical gene model annotations for that genome. These should therefore be the annotations that IGB automatically loads when a user visits a genome version for that species.
IGB QuickLoad is configured so the canonical gene models annotations are loaded into IGB as soon as the user selects the corresponding genome version.
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$ git clone https://bitbucket.org/lorainelab/genomesrcgenomesource |
If you already have a copy, then update it. Changed into your local copy and run:
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If you already have a copy, just update using svn up. Change into your checked-out, local copy and run:
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$ svn up |
Add
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quickloadsource to your PATH (to run the python code there)
Add quickloadsrc quickloadsource to your PATH as it contains a python script you'll use to created BED detail files from ordinary BED files. Edit the .bash_profile file as in above:
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export PATH=.:$HOME/quickload_srcquickloadsource:$HOME/bin:$PATH |
Pick a genome to update and change into the genome version directory
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Use ucscToBedDetail.py (from https://bitbucket.org/lorainelab/genomes_srcgenomesource) to create a new BED file with gene symbol and description
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