Hello! I am using nanopore RNA-seq to compare gene expression.
For some genes, my data set only have partially transcribed transcripts which lack reference_id attribute in StringTie's output record, but considered as "novel" as below. I am wondering if I could use some of the options to count these "novel" transcripts as the expression of an annotated gene (these "novel" transcripts overlap with genes).
Thanks!
Reference transcripts (guides)
Note that when a reference transcript is fully covered by reads, the original transcript ID from the reference annotation file will be
shown in StringTie's output record in the reference_id GTF attribute. Output transcripts that lack such reference_id attribute can be
considered "novel" transcript structures with respect to the given reference annotation.
Hello! I am using nanopore RNA-seq to compare gene expression. For some genes, my data set only have partially transcribed transcripts which lack reference_id attribute in StringTie's output record, but considered as "novel" as below. I am wondering if I could use some of the options to count these "novel" transcripts as the expression of an annotated gene (these "novel" transcripts overlap with genes). Thanks!
Reference transcripts (guides)
Note that when a reference transcript is fully covered by reads, the original transcript ID from the reference annotation file will be shown in StringTie's output record in the reference_id GTF attribute. Output transcripts that lack such reference_id attribute can be considered "novel" transcript structures with respect to the given reference annotation.