New to the bioinformatics world and first time post-er, so please excuse my ignorance.
Am working on a noncoding RNA project. Used STAR to align my reads, and attempted to use both Stringtie and Cufflinks to assemble. During Stringtie assembly, no reference annotation file was given, with all parameters at default aside minimum transcript length (set at 100).
IGV has done a half decent job so far at allowing me to visualise my Stringtie GTF outputs, but I was wondering if anyone had any other suggestions. I have just attempted to use RNAseqViewer on the same Stringtie output but I am getting an error that it isnt a valid GTF file.
Any advice appreciated, especially if I am missing something.