This is my first rna-seq data analysis project and I am using Galaxy to analyze differential expression on my RNA-seq data comparing 4 treatments. So far I have successfully trimmed my raw data using Trimmomatic, and aligned my reads using HISAT2. Now I am trying to use the htseq-count and was successful with my first few runs, but am now getting an error message for some files. I have tried re-running these several times and still end up with a failed run.
Should I abandon htseq and use another count tool or can I still use the data (that did not fail), discarding the failed files, to continue with my research?