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Question: Need help with "MPileup" tool
1
gravatar for charrison9
4.6 years ago by
charrison9 • 10
United States
charrison9 • 10 wrote:

I am trying to get SNPs and indels from a bowtie 2 on Illumina reads matched to the sinorhizobium meliloti (RM1021) genome using MPileup. When setting up the MPileup it asks for a reference genome. I can not find the sinorhizobium meliloti genome in the list of options. Is my genome in the list,but I don't know what it is called? Is there a way to add my reference genome to the list?

 

Tool name: MPileup
Tool version: 0.0.1
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.1
ToolShed URL: http://toolshed.g2.bx.psu.edu/view/devteam/samtools_mpileup

 
mpileup • 1.8k views
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modified 4.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.6 years ago by charrison9 • 10
1
gravatar for Jennifer Hillman Jackson
4.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

For smaller reference genomes, often the data is not indexed for all tools. Instead, simply upload the genome in fasta format into your history and use it as a Custom Reference genome and set the tool form option "Choose the source for the reference list:" to be "History". The form will change so that you can select the fasta genome dataset from the history.

Full instructions are here: https://wiki.galaxyproject.org/Support#Custom_reference_genome

Thanks! Jen, Galaxy team
ADD COMMENT • link written 4.6 years ago by Jennifer Hillman Jackson ♦ 25k
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