Moderator: venu

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venu6.3k
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Posts by venu

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Comment: C: Different number of peaks between biological replicates?
... Hi, > THe H3K27ac is my experience is especially problematic as it always gives rather poor quality data. H3K4me1 is typically better (=more specific in terms of signal/noise ratio). Is there any reference for this statement? IMO, poor quality must depend on IP efficiency or antibody quality or ...
written 11 days ago by venu6.3k
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Answer: A: DiffBind to call differential binding of Super-enhancers from ROSE
... You can pass custom count matrix to diffBind (check [reference manual, page 3: Construct a DBA object][1]). - For each sample make a bed file of super enhancers - calculate read counts from all your BAM files (using deepTools multiBamSummary function) - pass this to diffBind [1]: https:// ...
written 13 days ago by venu6.3k
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Answer: A: Distribution of mutations in different parts of the genome
... This is called `topography of mutations`. There are not many papers on this aspect of the mutations. One way is to follow this [paper](https://www.nature.com/articles/ncomms11383). You will get more insights if you do mutational signature analysis first and do genome distribution of these signatures ...
written 7 weeks ago by venu6.3k
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Answer: A: Motif analysis from H3K27ac ChIPseq broad peaks
... If the signals in IGV are looking reasonable over background for ~10kb domains, it is totally acceptable. There are something called **Super-enhancers** which are minimum of 10-12kb in size with high H3K27ac signal. Just google the term, you'll find number of papers solely based on super-enhancers. ...
written 8 weeks ago by venu6.3k
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Comment: C: qsea - genomic annotation
... annotate the windows with [ChIPseeker][1] [1]: https://www.bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html#peak-annotation ...
written 12 weeks ago by venu6.3k
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Tool: R pakcage: ALPS - AnaLysis routines for ePigenomicS data
... From a recent experience of working with epigenomics data for several projects, I have realized there can be a lot of data analysis tasks that require lines of coding. I found myself repeating some of these tasks and thought it makes sense to put some of these functions under one roof. The result ...
dataviz R epigenomics tool written 12 weeks ago by venu6.3k
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Comment: C: bedGraphToBigWig : command not found
... Try this ./bedGraphToBigWig tl.bedgraph hg38.chrom.sizes tl.bw Also do this before trying above command, chmod +x /home/anatoly/Epigenetics/Internship/assignment/* Not sure your command `chmod`s all contents of the directory. ...
written 3 months ago by venu6.3k
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Comment: C: History of Biostars
... I'd guess, many basic questions are being asked over the previous years and answered very well, so with a simple google search, first hits are landing on biostars threads. Also *many* tool developers are documenting their tools with clean examples and responding to the user queries. Might be saturat ...
written 8 months ago by venu6.3k
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Comment: C: History of Biostars
... Aw, your title makes more sense. Yes, I will try to make per-year frequency of tags (a good idea to see troubled topics per year :p). ...
written 8 months ago by venu6.3k
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Comment: C: History of Biostars
... Thanks Vijay. It may makes sense to get an overview of Tools per year, to check how frequently new tools are being developed. But what do you mean by `with application`? Because, each tool is flagged with more than one tag, so it's extremely complicated to get one-word application to each tool (by p ...
written 8 months ago by venu6.3k

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Appreciated 7 weeks ago, created a post with more than 5 votes. For A: Best bioinfo one-liners?
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Human Genome Project: Twenty-five years of big biology
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Scholar 7 months ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Popular Question 7 months ago, created a question with more than 1,000 views. For About Ion Proton Data
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Best bioinfo one-liners?
Popular Question 8 months ago, created a question with more than 1,000 views. For About Ion Proton Data
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: perl code to extract sequences from multi-line fasta works on all test files but
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Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Scholar 12 months ago, created an answer that has been accepted. For A: How to search Pfam DB using list of accessions
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Great Question 12 months ago, created a question with more than 5,000 views. For covert STOCKHOLM alignment to FASTA alignment
Popular Question 12 months ago, created a question with more than 1,000 views. For Help needed with selecting top DE genes, Microarray data analysed with "limma"
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