Question: Need help with "MPileup" tool
gravatar for charrison9
3.9 years ago by
United States
charrison910 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 URL:


mpileup • 1.6k views
ADD COMMENTlink modified 3.9 years ago by Jennifer Hillman Jackson24k • written 3.9 years ago by charrison910
gravatar for Jennifer Hillman Jackson
3.9 years ago by
United States
Jennifer Hillman Jackson24k wrote:


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:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 3.9 years ago by Jennifer Hillman Jackson24k
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