We are trying to analyze our files following this RNA Seq tutorial: https://galaxyproject.org/tutorials/nt_rnaseq/
Our DESeq2 outputs, however, are giving us MSTRG gene IDs, which are not very useful as the labels are only relevant internally. In researching how to convert MSTRG to a gene name, we found that a better “reference file to guide assembly” should be used to run StringTie so a gene name is outputted. However, the galaxy StringTie job fails when we use the Homo_sapiens_NCBI_GrCh38.tar.gz reference file. We have tried unzipping it to .tar and also using a DEXSeq annotation as the reference file, then ran StringTie, but this also failed. Also, the option to use a built in reference file is disabled. Currently, the only method that successfully outputs a DESeq2 file is when no reference file is used, however we are unsure how to convert the MSTRG gene ID it outputs to a gene name/prevent MSTRG outputs.
Any help is greatly appreciated; thanks in advance!