Question: Discovery of novel transcripts
0
gravatar for hana
4.2 years ago by
hana170
Malaysia
hana170 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 • 1.3k views
ADD COMMENTlink modified 4.2 years ago by Devon Ryan89k • written 4.2 years ago by hana170
2
gravatar for Devon Ryan
4.2 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k 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 4.2 years ago by Devon Ryan89k
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