I have encountered a problem with Galaxy analyses of RNAseq data when I want to analyze the differential expression using DESeq2 or EdgeR. Below are the typical error messages. I have used HISAT2 for as the alignment program, Stringtie for assembly, and both htseq count and featurecounts to count the reads. I have tried to use the output from either htseq count, featurecounts and Stringtie into DESeq2 or EdgeR with error messages popping up after a few minutes. The original data are from Illumina next seq, paired end. I am working with Galaxy Main https://usegalaxy.org.
Below is from DeSeq2
Fatal error: An undefined error occurred, please check your input carefully and contact your administrator. Error in data.frame(…, check.names = FALSE) : arguments imply differing number of rows: 51
Below from EdgeR
Fatal error: Exit code 1 () Error in data.frame(…, check.names = FALSE) : arguments imply differing number of rows: 51329, 58444, 53946 Calls: do.call -> cbind -> cbind -> data.frame