User: danvoronov
danvoronov • 10
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- Location:
- SZN, Naples, Italy
- Twitter:
- @danvoronov
- Last seen:
- 2 weeks, 5 days ago
- Joined:
- 1 year ago
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I am a biological sciences PhD student studying gene expression regulation with interest in bioinformatics at Stazione Zoologica Anton Dorhn, Naples, Italy.
Posts by danvoronov
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... You can also use knownResults.txt file from the `findMotifsGenome.pl` so this could be used for comparisons.
Alternatively try RGT motif analysis tool for differential motif analysis, although I don't think it can do de-novo predictions.
http://www.regulatory-genomics.org/motif-analysis/introduct ...
written 4 weeks ago by
danvoronov • 10
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... Hi,
If you want to do a feature plot you should have a UMAP or TSNE of clusters. So you need to make a Seurat object from the matrix, remove cells with low features, normalize the data, scale it, find variable features, run PCA analysis, find neighbors, then find clusters, finally fillowed by runni ...
written 4 weeks ago by
danvoronov • 10
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... Hello, you can use `bedtools makewindows -b -w 50 -s 25 > ` this will give you the sliding windows you want.
The Tn5 integration frequency is unclear, because you should have the fragments generated by the transposase "cutting" the genome, so I think you need 2 transposase reactions to generat ...
written 4 weeks ago by
danvoronov • 10
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