IGV view for Chromatin accessibility ATAC-seq

0

Entering edit mode

20 days ago

Vxike • 0

Hi All,

This is my first time to analyze ATAC-seq data. So after done with the typical pipeline, the final step is view Chromatin accessibility, for this, I using IGV. This is what I see (see attach pic), could you give some advice? is this normal? or something wrong with my analysis or my ATAC-seq data? Because usually I see sort of wavelet peak, but for me, I only see one "regtangle peak". Thanks

enter image description here

ATAC-seq • 346 views

ADD COMMENT • link updated 20 days ago by ATpoint 88k • written 20 days ago by Vxike • 0

1

Entering edit mode

How were these tracks generated? Is it bigwig files (or bedGraphs) at single-base resolution or was it like deeptools bamCoverage which by default uses a binsize of (I think) 50bp (so binning 50 adjacent bases into a single value) -- the latter would distort visually nice peaks into bulky rectangles as you see here.

I assume it's myeloid cells you look at ?

ADD REPLY • link 20 days ago by ATpoint 88k

Login before adding your answer.