SNP tool (Amino acid change) throwing error

Question: SNP tool (Amino acid change) throwing error

2.2 years ago by

sakhi_pujni • 10 wrote:

Hi I have discovered some 240,000 SNPs and am using the "amino-acid changes caused by a set of SNPs "tool to find out amino acid change if any in my SNPs. However whenever I try to use it i get an error sequences from the genome data-set build are not available.

1)I am using SNPs in interval format as an input data, 2) I am using BED 12 column (mapped to relevant dataset) as a gene dataset. Both of them have same gene dataset as the genome build but I get the same error.

Can anybody please advise me on this issue.

I want to remind you that I am using plant genome dataset if that is a cause of the problem.

Regards Sakhi

error tool custom-build custom-genome • 740 views

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modified 2.2 years ago • written 2.2 years ago by sakhi_pujni • 10

2.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

It is likely that the genome build assigned to the dataset is actually not available. Using a Custom Build will likely help. Make sure the formatting is strict fasta without annotation on the title lines.

How to promote a Custom Genome to a Custom Build: https://wiki.galaxyproject.org/Learn/CustomGenomes#Custom_Builds

Expected CG formatting and how to troubleshooting within Galaxy is also on the same wiki page.

Best, Jen, Galaxy team

ADD COMMENT • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k

2.2 years ago by

deepti.angra • 0

deepti.angra • 0 wrote:

Hello Jen Thankyou for your reply. I have added FASTA sequence without any annotation in the Custom Build (that I was using in my earlier steps) Now I have checked again but I still get the same error. Any thing else you can suggest me?

Sakhi

ADD COMMENT • link written 2.2 years ago by deepti.angra • 0

This new new "dbkey" for the Custom genome build was assigned as the "database" metadata attribute to all inputs? How-to: https://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset

This tool is a bit older and may not work with Custom Builds right now. If you want to send in a bug report I can double check and open an enhancement ticket. Make sure the inputs and tool run are undeleted until I can grab a copy (I'll reply to the bug email): https://wiki.galaxyproject.org/Support#Reporting_tool_errors

ADD REPLY • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen Can you precisely let me know how to share the history so that you can look in to it?

Sakhi

ADD REPLY • link written 2.2 years ago by deepti.angra • 0

2.2 years ago by

sakhi_pujni • 10

sakhi_pujni • 10 wrote:

Hi Jen

I will do so and share the history.

Sakhi

ADD COMMENT • link written 2.2 years ago by sakhi_pujni • 10

2.2 years ago by

sakhi_pujni • 10

sakhi_pujni • 10 wrote:

Hi Jen

I am unable to send the bug report as the tool shows en error and no update in the history. You can crop in to my history and have a look. What other way can i send you the bug please let me know.

Thanks Deepti

ADD COMMENT • link written 2.2 years ago by sakhi_pujni • 10

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