Question: Facing trouble to analyze the different Rice genes on David Bioinformatics Resources 6.8
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gravatar for rj.rezwan
2.6 years ago by
rj.rezwan0
rj.rezwan0 wrote:

Hi, I am dealing with Rice for RNA-Seq analysis. Nowadays, I am facing an issue at David bioinformatics resource 6.8. Actually, I was quite comfortable to analyze the DEGs (differentially expressed genes) data on David version 6.7, but I am facing trouble on 6.8 with the same set of genes which were analyzed on David 6.7. Could anyone help me to get rid of this trouble?

Source: Rice genes were retrieved from Rice annotation project database (Rap-db). Select identifier option in David 6.8 and 6.7: official gene symbol.

rna-seq david 6.8 • 743 views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by rj.rezwan0

I am facing an issue

I am facing trouble

help me to get rid of this trouble?

So, what's the problem?

ADD REPLYlink written 2.6 years ago by WouterDeCoster44k

I am used to analyzing the differentially expressed genes for functional annotation in David bioinformatics resource. Now, David page has been updated from version 6.7 to 6.8. This 6.8 version (updated) is not analyzing the differentially expressed rice genes for functional annotation, and the set of genes are same, analyzed in David 6.7. So the question is this, why updated version (6.8) is not accepting the previously analyzed genes and gives the error, "You are either not sure which identifier type your list contains, or less than 80% of your list has mapped to your chosen identifier type. Please use the Gene Conversion Tool to determine the identifier type."

But I have analyzed data in David 6.7 using same identifier type option. When I used the conversion tool, it just converted two genes from >2000 genes. It means David 6.8 version will give again error if I use transcriptomic data of rice from another experiment.

ADD REPLYlink written 2.6 years ago by rj.rezwan0

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. Your comment should have been under mine. I have now moved your reaction but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

Please add an example of gene names that used to work, but don't work any more. You must realize that we cannot see what happens on your computer, so sharing examples and error messages is very important to get accurate help. This longer explanation, examples and error message should have been part of your initial question to avoid wasting time.

ADD REPLYlink written 2.6 years ago by WouterDeCoster44k

Here, I have attached the links to four step by step snapshot of the David tool 6.8. Hopefully, it would be easy for you to understand my problem.

https://ibb.co/ncaww7 https://ibb.co/f6PpG7 https://ibb.co/dE8ib7 https://ibb.co/haJc3n

ADD REPLYlink written 2.6 years ago by rj.rezwan0

See also How to add images to a Biostars post

On each screenshot there is a link to David 6.7, so that should be sufficient to solve your issue. Perhaps David 6.8 is still under development.

ADD REPLYlink written 2.6 years ago by WouterDeCoster44k

Thanks a lot for helping me.....

ADD REPLYlink written 2.6 years ago by rj.rezwan0

David 6.8 is marked as "development", but I'd suggest contacting the maintainers directly if you see differences like this between 6.7 and 6.8.

ADD REPLYlink written 2.6 years ago by WouterDeCoster44k

Thanks.Got your point.

ADD REPLYlink written 2.6 years ago by rj.rezwan0
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