Need help with "Realigner Target Creator" tool

Question: Need help with "Realigner Target Creator" tool

4.1 years ago by

davidvanbruggen • 0

Netherlands

davidvanbruggen • 0 wrote:

Hi every one,

If somebody familiar with using the GATK realigner target creator on galaxy?

My data is not supported on galaxy I assume. The tool is giving me two problems;

Sequences are not currently available for the specified build.

-I,--input_file <input_file>

A built-in reference genome is not available for the build associated with the selected input file

-R,--reference_sequence <reference_sequence

My data is single read illumina data, BWA mapped to hg19, reordered BAM file with marked duplicates PICARD.

Does anybody have suggestions on what to do next?

cheers,

David

Tool name: Realigner Target Creator
Tool version: 0.0.4
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/realigner_target_creator/gatk_realigner_target_creator/0.0.4
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/devteam/realigner_target_creator

realigner-target-creator • 1.9k views

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modified 4.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.1 years ago by davidvanbruggen • 0

4.1 years ago by

davidvanbruggen • 0

Netherlands

davidvanbruggen • 0 wrote:

I think I fixed the problem by importing hg19 in galaxy history through the top button shared data > data libraries > GATK > hg19 (click import into history). Now it should accept the reference genome. And snp files can be imported into history as well.

cheers,

David

ADD COMMENT • link modified 4.1 years ago • written 4.1 years ago by davidvanbruggen • 0

4.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi,

I am glad the analysis is working out. A few things to be aware of, and I am not sure if this was part of your issue or not, is the difference between 'reference annotation' and 'reference genome'. I'll share anyway just for other readers.

reference genome: specific version of an assembly that represents the genome in nucleotide space. this is the fasta dataset used in Galaxy with tool forms when using a Custom reference genome, creating a custom build, etc.

--> on a tool form, there are a few way to enter this data, the above is in this category
much more about Custom genomes -
http://wiki.galaxyproject.org/Support#Custom_reference_genome

reference annotation: defines features present on a specific version of a reference genome. Common formats: gtf, gff, gff3. Please be aware that gff3 can include the fasta content of the features at the end of the file. This is in specification, but when using in Galaxy, only include the annotation lines. This is what you found in the shared data library.

--> much more about RNA-seq
http://wiki.galaxyproject.org/Support#Tools_on_the_Main_server:_RNA-seq

Best, Jen, Galaxy team

ADD COMMENT • link written 4.1 years ago by Jennifer Hillman Jackson ♦ 25k

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