Moderator: venu

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venu6.6k
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Posts by venu

<prev • 730 results • page 1 of 73 • next >
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Comment: C: Setting Peak Cutoff Using Minimum # of Reads
... That's a usual problem with differential analyses. Along with fold change, use normalized read count (e.g. RPM) as the cut off, e.g. min RPM must be >5. ...
written 17 hours ago by venu6.6k
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Comment: C: how to extract mutation from MAF file in python
... `MAF` is already a mutation file. What do you mean by extract mutations? ...
written 24 days ago by venu6.6k
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Comment: C: Split up a matrix into chunks considering the values of a column in Bash
... I'm not providing the code, but here is what you can do prepare a list object where each element of the list contains gene names, e.g. gene_names_list $chunk1 ENSG1 ENSG2 ENSG3 $chunk2 ENSG4 ENSG5 ... Loop over this list object and collect your matrix chun ...
written 7 weeks ago by venu6.6k
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Comment: C: How do I load a peak file in ChIPseeker?
... May be, by learning basics of R? ...
written 8 weeks ago by venu6.6k
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Comment: C: How do I load a peak file in ChIPseeker?
... From the docs, if you look at the code files <- getSampleFiles() print(files) `files` is a named list object with paths ti bed file. So you need to create such an object with your files. ...
written 9 weeks ago by venu6.6k
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Comment: C: Virus Genome Length and GC Content of SARS-COV-2 causing COVID-19
... Hi Dulankak, I'd suggest you add updates within your original thread instead of posting as answer each time when there is a new release. ...
written 9 weeks ago by venu6.6k
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Answer: A: Have we failed as bioinformatician in this time of COVID-19
... Hi Heididunst, my few points > It about more than 5 months for COVID-19 pandemic but still we far from developing any vaccine If we look at time needed for vaccine development (for previous diseases), one might understand it's not possible to get something reasonable in the span of 1 year, let ...
written 9 weeks ago by venu6.6k
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Comment: C: Annotation of acetylation ChIP-seq peaks to the nearest gene and reads cont
... Differential expression? Or differential enrichment of acetylation? If it's later, just do differential enrichment analysis with all peaks and annotate the differential peaks, that'd be a better option. ...
written 9 weeks ago by venu6.6k
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Comment: C: Annotation of acetylation ChIP-seq peaks to the nearest gene and reads cont
... If I may ask, what's the next step in your analysis? Because, I don't see any problem if more than one peaks is annotated to single gene, especially for acetylation peaks. You might want to check literature on super-enhancers to collapse close by peaks into one single region. Having said that, if y ...
written 9 weeks ago by venu6.6k
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Answer: C: Clustering with Jaccard Distance
... Why not take variably expressed genes across all samples and do clustering? I am not sure of exact reasons, but your approach doesn't seem what you want for the results you are expecting. For example, from RNA-seq some genes, such as ribosomal genes/house keeping genes always have higher read coun ...
written 10 weeks ago by venu6.6k

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Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: perl code to extract sequences from multi-line fasta works on all test files but
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