Question: SNP tool (Amino acid change) throwing error
1
gravatar for sakhi_pujni
21 months ago by
sakhi_pujni10
sakhi_pujni10 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

ADD COMMENTlink modified 21 months ago • written 21 months ago by sakhi_pujni10
0
gravatar for Jennifer Hillman Jackson
21 months ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 21 months ago by Jennifer Hillman Jackson25k
0
gravatar for deepti.angra
21 months ago by
deepti.angra0 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 COMMENTlink written 21 months ago by deepti.angra0

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 REPLYlink written 21 months ago by Jennifer Hillman Jackson25k

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

Sakhi

ADD REPLYlink written 21 months ago by deepti.angra0
0
gravatar for sakhi_pujni
21 months ago by
sakhi_pujni10
sakhi_pujni10 wrote:

Hi Jen

I will do so and share the history.

Sakhi

ADD COMMENTlink written 21 months ago by sakhi_pujni10
0
gravatar for sakhi_pujni
21 months ago by
sakhi_pujni10
sakhi_pujni10 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 COMMENTlink written 21 months ago by sakhi_pujni10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 128 users visited in the last hour