Bedgraph Signal Along Introns

Question

[GPR]

Hello, I have created a bedgraph from the transcripts.gtf file produced by cufflinks. When I upload this bedgraph on any genome viewer (IGV. IGB, SAVANTH, UCSC), I consistently see FPKM signal entirely across each transcript. Is it normal to see this? Am I missing something? I did run cufflkinks with the option -j set at 0.01, to filter out intronic reads. Thanks G.

Answer 1

[JC]

You always see a little signal (maybe because the protocol also captures pre-mRNA forms, specially in non-polyA selection protocols), but if you are seeing a LOT of signal, maybe indicate a problem. How much is the intronic expression that you see compared with the exon expression? A plot could be great.