Changes between Version 3 and Version 4 of SOPs/genome_regions_annotations

Timestamp:

10/22/13 10:22:13 (11 years ago)

Author:

gbell

Comment:

--

SOPs/genome_regions_annotations

@@ -120 +120 @@
 On Whitehead servers, pre-installed genomes (with annotations) can be chosen from the directory names in /usr/local/share/snpEff/data
 
-Creating a novel database for snpEff
-  * Make a copy of the snpEff config file containing the path to your new database (ex: ~/snpEff/data/myGenome.v1)
-  * In that directory (ex: data/myGenome.v1) put the genome (called ''sequences.fa'') and a GTF file describing the genes (called ''genes.gtf'').
-  * Go to that directory and run
-      * java -jar /usr/local/share/snpEff/snpEff.jar build -gtf22 -v myGenome.v1
-  * Now there should be a new file: data/myGenome.v1/snpEffectPredictor.bin
+Creating a novel genome database for snpEff:
+
+  * Check if the genome database has been installed: 
+      * cd /usr/local/share/snpEff
+      * java -jar /usr/local/share/snpEff/snpEff.jar databases
+  * If not already installed, check if the genome has been processed for snpEff at http://snpeff.sourceforge.net/download.html#dblist
+  * If you need to create it yourself, do the following:
+    * Make a copy of the snpEff config file containing the path to your new database (ex: ~/snpEff/data/myGenome.v1)
+    * In the config file directory (ex: data/myGenome.v1) put the genome sequence (called ''sequences.fa'') and a GTF file describing the genes (called ''genes.gtf'').
+    * Go to that directory and run
+        * java -jar /usr/local/share/snpEff/snpEff.jar build -gtf22 -v myGenome.v1
+    * Now there should be a new file: data/myGenome.v1/snpEffectPredictor.bin