This is my first time using Galaxy. I am currently trying to perform Differntial Expression Analysis with Small RNA Seq data and I am having issues with running EdgeR.
I have followed this pipeline:
Align with MirDeep2 Mapper
Quantify teads with MirDeep2 Quantifier
Cut columns belonging to miRNA ID and read counts and generate a new file.
Perform Differential Expression Analysis with Deseq2 with this new file.
After performing reads quantification with MirDeep2 Quantifier, I obtained the following count table:
After that, I cut the columns 1 and 2 with ´cut columns from a table´tool, and used this new table to perform DEA with Deseq2. After the cutting, the table looked like this:
However, when I tried to run this cutted tables with EdgeR it indicates this error:
Error in read.table(file = file, header = header, sep = sep, quote = quote, :
duplicate ‘row.names’ are not allowed
I understand this is because more than one microRNAs can have the same ID and come from differente precursors. However, I don´t know which is the best way to solve this problem. I have read other comments in this issue but couldn´t find a solution until now.
Thank you very much in advance for you help!