diff snpEff_macros.xml @ 15:479c4f2f4826 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173

--- a/snpEff_macros.xml	Tue Jun 12 17:31:21 2018 -0400
+++ b/snpEff_macros.xml	Mon Jul 09 13:22:58 2018 -0400
@@ -54,11 +54,11 @@
 
 In cases when you are dealing with bacterial or viral (or, frankly, any other) genomes it may be easier to create database yourself. For this you need:
 
- #. Download Genbank record corresponding to your genome of interest from NCBI.
+ #. Download Genbank record corresponding to your genome of interest from NCBI or use annotations in GFF format accompanied by the corresponding genome in FASTA format.
  #. Use **SnpEff build** to create the database.
  #. Use the database in **SnpEff eff** (using *Custom* option for **Genome source** parameter).
 
-Creating custom database has one benefit. The **SnpEff build** tool normally produces two outputs: (1) a SnpEff database and (2) FASTA file containing sequences from the Genbank file. If you are performing your experiment from the beginning by mapping reads against a genome and finding variants before annotating them with SnpEff you can use **this FASTA file** as a reference to map your reads against. This will guarantee that you will not have any issues related to reference sequence naming -- the most common source of SnpEff errors.
+Creating custom database has one major advantage. It guaranteess that you will not have any issues related to reference sequence naming -- the most common source of SnpEff errors.
 
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