Hi, I have recently started to analyse RNAseq data using StringTie "transcript assembly and quantification" on Galaxy (https://usegalaxy.org/). My aim is to identify and quantify transcript variants for my genes of interest. For this, I ran a single .bam file, using a gencode (.gtf) file as a reference. Looking at one of my genes of interest in the “assembled transcripts” file, I observed several transcripts annotated in Ensembl!. However, when I looked at the same gene (from the same .bam file analysis) in the “fully covered transcripts file”, I noticed an additional transcript, which was not present in the “assembled transcripts file”. I do not understand how it is possible for a transcript to be absent from the assembled transcript file, but present as a fully covered transcript in a different file? I am very new to this, so there is most likely a logical explanation I am missing. I’ve looked elsewhere but haven’t found the answer. Therefore, any help would be very appreciated. Many thanks! Florian
