Enhancer prediction for Glioma Stem Cells (ChIP-Seq)

0

Entering edit mode

4.7 years ago

Kasthuri ▴ 300

I am trying to predict enhancer regions in the ChIP-Seq data derived from Glioma Stem Cells (human). I already have aligned the data to hg19 and called the peaks. I understand ChromHMM and Encode annotations for histone marks may do the trick but I am lost on the step by step procedure since this cell line is not covered in any of the state models.

Any help will be much appreciated on either using ChromHMM or annotation packages. Thanks.

ChIP-Seq Enhancer • 1.2k views

ADD COMMENT • link 4.7 years ago by Kasthuri ▴ 300

0

Entering edit mode

What ChIP-Seq data do you have ?

ADD REPLY • link 4.7 years ago by GouthamAtla 12k

0

Entering edit mode

Do you mean like the file format? - It is bed format. It's from human-derived glioma stem cells (GSCs) - both control and experiment. Is this what you are asking?

ADD REPLY • link 4.7 years ago by Kasthuri ▴ 300

0

Entering edit mode

What ChIP data it is ? Histone modifications ? TFs ?

ADD REPLY • link 4.7 years ago by GouthamAtla 12k

0

Entering edit mode

No, not histones. TFs - knock out of a gene -

ADD REPLY • link 4.7 years ago by Kasthuri ▴ 300

Login before adding your answer.