Hi, first of all, thank you for existing ! I am somewhat new to bioinformatics but i've learned much in the last year. I am familiar with running RNAseq pipelines in order to get differentially expressed genes using DEseq, HTSeq, cufflink, EdgeR etc...BUT, I am facing something new; I have total RNAseq data and would like to see if some long non-coding RNAs are differentially expressed in my patients. I have their positions and their sequences. But they are not "identified" in databases so they're not part of the gene reference file.
My question is: is it possible at all to get differential expression based off of sequences ?
Would I have to manually change my gene.gtf ?.. Any help would be welcome.
Thank you very much