I am new to Galaxy, and am trying to complete a differential gene expression analysis. I use two replicates of RNAseq data. Since I got the clean reads data, I started my workflow from HISAT2>>StringTie>>StringTie merge>>StringTie (using Stringtie merge as a reference genome) >> DESeq2. I found an error result of DESeq2, and then I checked my input, and I found that some of the StringTie gene counts of my data were showing 0 counts. I don’t know why this happened, because the other data is good. Can anyone help me out with this problem? Thanks!
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