diff --git a/doc/admin.rst b/doc/admin.rst index 0dad3f0468801f82c57f7adcab199bb0e5f33164..ac3a86f7925bbd980ffe92a112ab87d319996e57 100644 --- a/doc/admin.rst +++ b/doc/admin.rst @@ -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 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^