Discovery of novel transcripts

Question

[hana]

I would like to identify of novel transcripts from my RNA seq data by cufflinks. How can I filter those that are overlap with RNA polymerase II binding sites?

Thank you

Answer 1

[Devon Ryan]

1. Find a PolII ChIP-seq dataset from whatever cell-line or tissue you're using. If one doesn't exist, you'll have to either generate it or find a dataset that's similar enough to be useful.
2. If you can't simply download peak calls then you'll have to call them yourself.
3. Use bedtools, bedops, or even just R to find TSSs from your dataset that are within some window of the aforementioned peaks.

[Pranathi]

How do I identify novel transcripts after attaining stringTie merged gtf files?