import of refrence genome

Question: import of refrence genome

13 months ago by

k_s_87 • 0

k_s_87 • 0 wrote:

How can I add reference human genome to local galaxy instance? I've got fasta file and bwa index, but how can I upload it to the data mannager?

thanks kate

rna-seq • 407 views

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modified 13 months ago • written 13 months ago by k_s_87 • 0

13 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Even if you already have the human genome, you might want to let the Data manager fetch the genome from the source (if it is a source listed on the DM). Or you can put your fasta version into the same history that you run DMs from, and input the fasta on the DM form as the "source from the history".

Rerunning the DM for BWA would be an easier way of getting the index into Galaxy (instead of manually adding in an existing index). But this is your decision.

Both choices are explained here, plus there is a DM tutorial: https://galaxyproject.org/admin/#data-resources

Thanks! Jen, Galaxy team

ADD COMMENT • link written 13 months ago by Jennifer Hillman Jackson ♦ 25k

13 months ago by

k_s_87 • 0

k_s_87 • 0 wrote:

Hi, Thanks for your answer. I did as you mentioned and there is both reference genome (.fa) and index in data library. However, when I want to use FreeBayes tool, there is no option to use my local reference genome. How can I fix it?

Thanks, Kate

ADD COMMENT • link written 13 months ago by k_s_87 • 0

Any genome added to fasta_indexes.loc will be available to Freebayes. The tool does not use special tool-specific indexes.

You can also select a genome/transcriptome/exome (really any fasta target) "from the history" with this tool to create an index during runtime. As is with most Galaxy tools. How to: https://galaxyproject.org/learn/custom-genomes/

ADD REPLY • link modified 13 months ago • written 13 months ago by Jennifer Hillman Jackson ♦ 25k

Hi - Dan from our team reminded me that running Samtools indexes on an already fetched genome also populates the table that Freebayes uses for indexes. So try doing that.

I tend to load all genomes with these DMs, in this order:

1 - Fetch 
2 - Samtools 
3 - Picard
4 - 2bit
5 - Other tool-specific indexes (BWA, etc), any order

This helps to make sure most tools/functions get baseline data index files/tables installed and usable. Those that 1) come default in Galaxy or 2) are imported from the tool shed but do not have a specific data manager or index instructions the author added to the README. You can always look at the tip files for a repo for that info to check to see where it is getting index data by table name. This one is a bit confusing but most others match up well.

I keep track making indexes for http://usegalaxy.org in a ticket which might help. You can also see the open minor issues that have come up (linked tickets). https://github.com/galaxyproject/galaxy/issues/1470

ADD REPLY • link modified 13 months ago • written 13 months ago by Jennifer Hillman Jackson ♦ 25k

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