Question: Snippy does not recognize my genbank reference file
0
gravatar for grchen
4 months ago by
grchen0
grchen0 wrote:

Hi, I'm using snippy to look for SNPs in my bacterial genomes. Snippy does not seem to be able to recognize my reference genome.gb file (obtained from NCBI). The sample .gbk file from Galaxy's microbial variant calling tutorial is recognized by snippy. Also using a fasta file of my genome works, but I lose gene information. Am I using the wrong file type or am I uploading the files incorrectly to Galaxy?

ADD COMMENTlink modified 4 months ago by d.hand0 • written 4 months ago by grchen0
0
gravatar for Jennifer Hillman Jackson
4 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Quote from the tool form:

--reference [X] Reference genome. Supports FASTA, GenBank, EMBL (not GFF) (default '')

The tool accepts genbank formatted data. If it is not finding your dataset(s), check to make sure the datatype is set correctly. This is how: https://galaxyproject.org/support/

I am not exactly sure how this tool works but if that is not enough (although it should be) you could try changing the file extension to .gbk and see if that works. If that is the solution - the tool author can be contacted about the problem through the Tool Shed. This would be considered a bug, but a minor one, with a workaround. Correct datatype assignment should be enough - dataset names should be ignored, with names/extensions used only as labels.

If the tool doesn't work after that, then it depends on where you are using Galaxy. If at some public Galaxy server, contact information is generally on the home landing page. If this your own Galaxy, start by checking the tool install for problems and making sure that Galaxy is current: https://docs.galaxyproject.org/en/master/releases/18.01_announce.html

Thanks! Jen, Galaxy team

ADD COMMENTlink written 4 months ago by Jennifer Hillman Jackson25k
0
gravatar for d.hand
4 months ago by
d.hand0
d.hand0 wrote:

NCBI has an option to download genomes in genbank format .gbk. This is how I got my annotations for snippy.

ADD COMMENTlink written 4 months ago by d.hand0
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