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Published 20 hours ago • verified publisher icon loosolab

DNase-seq

Open huangyingzhang opened this issue 2 years ago • 1 comments

Is the "TOBIAS ATACorrect" suitable for DNase-seq where DNase I cut the chromatin?

huangyingzhang avatar Jun 15 '22 08:06 huangyingzhang

Hi,

Good question - I have not used it for DNase-seq myself, but theoretically, yes! You might want to adjust the parameters of ATACorrect to --read-shift 0 0 and --k_flank 6, as the DNase bias motif is not shifted and is smaller than the one for Tn5.

I would be interested to hear your experience, if you end up using it. Please let me know :-)

msbentsen avatar Jun 17 '22 09:06 msbentsen