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mutalyzer
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6c6241e6
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6c6241e6
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9 years ago
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Vermaat
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Add docs for LRG transcripts mapping import
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@@ -73,6 +73,20 @@ Examples for other assemblies can be found in `this Gist
<https://gist.github.com/martijnvermaat/ce84945d05b4e42d3584>`_.
Import mappings from an EBI LRG transcripts map file
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The EBI provides `FTP downloads <ftp://ftp.ebi.ac.uk/pub/databases/lrgex/>`_
of transcript mappings for all of the LRG sequences on the latest human genome
assembly. These can be imported with ``mutalyzer-admin``.
For example, to import LRG transcript mappings for the GRCh37 assembly, run
the following::
$ wget ftp://ftp.ebi.ac.uk/pub/databases/lrgex/list_LRGs_transcripts_GRCh37.txt -O /tmp/hg19.lrgmap.txt
$ mutalyzer-admin assemblies import-lrgmap -a hg19 /tmp/hg19.lrgmap.txt
Import mappings from the UCSC Genome Browser MySQL database
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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