I have downloaded an RNAseq dataset .BAM files with the pyega3 tool at EGA.
I have also downloaded the .tar file that lists the experiments, runs, etc but do not see a .gtf or .gff file to run something like featureCounts on the BAM files.
Any input appreciated, feel like there may be an easy answer here.
Thanks for your directions.
I then downloaded the .GTF file from ensemble. Thanks.
To your revert to fastq, I did not do that but it was recommended as several pipelines start with fastq files.