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Hi
we do not think this is a dbTF. The zinc finger is a ubiquitin like fold and therefore unlikely to bind dsDNA, and instead protein interaction domain.
Please delete these rat annotations
MGI…
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>[HOMER]( http://homer.ucsd.edu/homer/)(Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. It is a collection of command line p…
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We need to double-check the methods section, including disambiguating the various labware, "deepwell" or not.
@daneckaw has agreed to do this by next week (11th June). Then we should kick back over…
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Hi,
could you please suggest how to do a differential DHSs analysis ?
I can see that the output is a matrix of DH levels as gene by sample. I understand the "level" is normalized with a default …
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https://mp.weixin.qq.com/s/YZlwlcVgFkiwifbmnmgC6g
ixxmu updated
2 years ago
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Hi,
Is it possible to use `gimmemotifs` for the detection of RNA motifs from CLIP-seq derived locations? Off the top of my head, the main differences from ChIP-seq (DNA) motifs is that RNA motifs w…
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Meeting note on Feb 26. 2021
1. DNA footprinting pipeline(shared by Shannon): http://www.regulatory-genomics.org/hint/introduction/
2. DNA footprinting paper (shared by Shannon): https://genomebiolo…
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## Bi-weekly meeting memo
0. Files that Shannon will share to Tao
- ATAC-seq datasets: fastq
- variant dataset: vcf
- packages: R Bioconductor, ChIPPeakAnno, ChipSeerker
1. make the footprint f…
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Hi,
Thanks a lot for the great tool and nice vignettes, which are super helpful!
I have a question regarding your RNA+ATAC tutorial (http://htmlpreview.github.io/?https://github.com/welch-lab/li…
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https://mp.weixin.qq.com/s/4-SUn7JGbnWlR4N5ekebtQ
ixxmu updated
3 years ago