Hello, I am trying a build a workflow for RNA-Seq analysis and I want to verify my methods via comparing a data set. The data sets I am trying to use are GSE56016 and GSE36537 from NCBI GEO. They have only one RNA-Seq result. I downloaded fasta from EBI SRA did analysis. I used TopHat and want to compare the accepted hits results. The results from NCBI GEO includes gene names in accepted hits files but my result does not have any gene names. I converted them to BED files via BAMtoBED tool but I still do not have any gene names.
How can I extract the gene names from accepted hits files?