Question: Discovery of novel transcripts
gravatar for hana
5.8 years ago by
hana180 wrote:

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 • 1.7k views
ADD COMMENTlink modified 5.8 years ago by Devon Ryan97k • written 5.8 years ago by hana180
gravatar for Devon Ryan
5.8 years ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:
  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.
ADD COMMENTlink written 5.8 years ago by Devon Ryan97k
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