Discovery of novel transcripts

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

rna-seq

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updated 4.3 years ago by Ram

• written 11.5 years ago by hana

1 answer

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.
If you can't simply download peak calls then you'll have to call them yourself.
Use bedtools, bedops, or even just R to find TSSs from your dataset that are within some window of the aforementioned peaks.

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updated 4.3 years ago by Ram

• written 11.5 years ago by Devon Ryan

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

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written 5.4 years ago by Pranathi •

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