Hi, I am having following goseq error while using two inputs shown below:
As a genome file I used both gtf and fasta files of the potato genome but the error message has not changed (the file format was not indicated in the tutorial).
How should I proceed?
this history reproduces the analysis in which you have faced difficulties: history goseq. I suggest you have a look at it, probably you will find the cause of the problem. If you cannot find the problem, please share your history with me.
@galladoalba I could not find what the problem is. I tried the analysis on eu server as you shared; however, no idea about why I am having this problem. One more thing, you said :
what do you mean with that? Does the analysis in EU server affects analysis in AU server?
I am leaving the link in case that you want to see the history of the analysis :
the problem is that Limma goseq requires inputs ( differentially expressed genes file and gene lengths file) of the same number of entries; in order to fix the problem, you need to run Limma without filtering low expressed genes.
Now, I understand in my length file I have more than 30000 genes whilst only about 25000 genes are available… I will run the analysis again with equal number of genes, I will let you know if it works… heartfelt thanks.
Nope… it did not work out.
Could you share your history with me again, please?
To help you understand my doings, let me explain how I proceeded.
I merged all data files as you can see in 11. and I created status and length files by cutting necessary columns. Then I ran the goseq
the result was the same error message. The link is below.
in that case the problem is that the gene annotation file should have this format: annotation file.
This paper provides some information about how to obtain the GAF (Go Annotation File) corresponding to S. tuberosum.
Heartfelt thanks for all your help