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User: danvoronov

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danvoronov • 10
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10
Status:
New User
Location:
SZN, Naples, Italy
Twitter:
@danvoronov
Last seen:
3 months, 2 weeks ago
Joined:
2 years, 4 months ago
Email:
d***********@gmail.com

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

<prev • 7 results • page 1 of 1 • next >
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Gviz histogram plot height
... I want to make a plot with Gviz for my bedgraph tracks, bed files and gff annotation. I have this command for plotting bedgraph tracks: bg1 <- DataTrack( range = file, name="gene", type = "histogram", fill.histogram = "magenta", col.histogram = shade, window=-2, windowSize=2, ...
R chip-seq gviz plots written 3 months ago by danvoronov • 10
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Genome aligner that shows annotations too
... Hi, I am looking for a tool that can align two closely related eukaryotic genomes (or parts of the genomes, because the genomes themselves are quite large). I also need this tools to show genome annotations, such as genes or BED regions along with the alignments. Can anyone suggest anything? Thank ...
genome alignment annotations written 12 months ago by danvoronov • 10 • updated 11 months ago by Biostar ♦♦ 20
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Trinity transcriptome assembly
... Hi, Sorry, does anyone know if it is possible to run Trinity de-novo assembly using both FASTA and FASTQ files as input? Thanks. Best, Dan ...
trinity rna-seq assembly written 15 months ago by danvoronov • 10 • updated 15 months ago by h.mon ♦ 32k
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Comment: A: What to think about when treating scRNA-Seq data as bulk RNA-Seq data
... I was wondering if it was possible to use one or more of the FASTQ files (if you have 10x genomics), try FASTQC to see if there are any adaptors and bad reads, and then try to use it straight to map onto genome as a normal bulk RNA-seq, or Trinity if no genome is available? If you only have one samp ...
written 16 months ago by danvoronov • 10
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Answer: A: Finding differences in motif enrichment between ATAC peak samples?
... 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 17 months ago by danvoronov • 10
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Answer: A: read a scRNA-seq matirx with Seurat
... 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 17 months ago by danvoronov • 10
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Answer: A: ATAC-seq macs2 peak splitting in sliding windows
... 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 17 months ago by danvoronov • 10

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