Hi
I am trying to analyse RNA-seq data on Galaxcy.eu.
Uproad->Trimmomatic->FastQC->HISAT2->featureCount->annotate
I have done up to.
When I tried to process the data in Limma-voom, I got an error.
Tool Standard Error shows this
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
line 1492007 did not have 10 elements
Calls: read.table → scan
Execution halted
Can someone please give me some advice that a beginner can understand?
Thanks.
Hi @hashimoto.takuma
Have you merge the data into a table or do you use individual count files? Do you have identical number of lines in the count files? I am also curious about annotation. By any chance do you have missing values? I am somewhat puzzled with ‘line 1,492,007’: this number is too big for gene number.
Maybe consider a test limma-voom run using outputs of featureCounts, without annotation. Also, consider this tutorial: 2: RNA-seq counts to genes
If this does not help, I can check the data, if you share the history with me. History sharing: History menu (at the top of the history panel) > Share or publish > Make history accessible > copy the URL and past it in reply. Before sharing you can copy relevant files into a new history.
Kind regards,
Igor