As a new one on Bioinfo world, I'm experiencing dificulties while learning about. I have a RNA-seq (Illumina 75-100bp) dataset and I used our lab's reference de novo transcriptome to align it and produce a estimation of gene/transcripts expression with RSEM. So, I was planning to work downstream with the RSEM output as input for edgeR, but now I know that isn't the best thing to do. Now I'm planning working with htseq -> DESeq2, but for htseq it's necessary a GFF/GTF file as input, and as we only have a de novo transcriptome assemble, I'm pretty confused now, even after reading about it. Is it possible to create a GFF from this assemble? If I align (bowtie way) my libraries to the reference, would be possible to create a GFF from the .sam output file? Also, is it possible working with htseq without a GFF as an alternative?
To note, this is the way our reference looks like:
Thanks in advance!