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comparison snpEff_macros.xml @ 15:479c4f2f4826 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
author iuc
date Mon, 09 Jul 2018 13:22:58 -0400
parents 5a29ab10dba6
children 65ae79bddc69
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14:85ca751407c3 15:479c4f2f4826
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53 **Create your own database** 53 **Create your own database**
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55 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: 55 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:
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57 #. Download Genbank record corresponding to your genome of interest from NCBI. 57 #. 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.
58 #. Use **SnpEff build** to create the database. 58 #. Use **SnpEff build** to create the database.
59 #. Use the database in **SnpEff eff** (using *Custom* option for **Genome source** parameter). 59 #. Use the database in **SnpEff eff** (using *Custom* option for **Genome source** parameter).
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61 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. 61 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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