Question: Need help with "MPileup" tool
gravatar for charrison9
4.6 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 • 1.8k views
ADD COMMENTlink modified 4.6 years ago by Jennifer Hillman Jackson25k • written 4.6 years ago by charrison910
gravatar for Jennifer Hillman Jackson
4.6 years ago by
United States
Jennifer Hillman Jackson25k 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 4.6 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 175 users visited in the last hour