User: BioinformaticsBro

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Posts by BioinformaticsBro

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Comment: C: Plotting MBD-seq results
... Very helpful, thanks! I wonder if you'd also know what package to use for performing GO annotations on MEDIPS results? I'd like to do GO annotations so I can visualize the results with clusterProfiler. ...
written 2 days ago by BioinformaticsBro10
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Comment: C: sam file not showing multi mapped reads
... How would it determine what the 'best' mapping is if both regions are (as in this toy model) exactly the same? My initial guess is that it would simply report the first mapping if there are two equally good mappings. But in the above example, copy 2 is reported. Maybe after indexing, copy 2 is place ...
written 2 days ago by BioinformaticsBro10
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Plotting MBD-seq results
... Does anyone know of any programs or R packages to plot MBD-seq methylation status results like this? Thanks! I'm using the R package MEDIPS for my analysis. ![enter image description here][1] [1]: https://www.researchgate.net/profile/Alika_Maunakea/publication/271333734/figure/fig2/AS:61637969 ...
methylation mbd-seq written 5 days ago by BioinformaticsBro10 • updated 5 days ago by cmdcolin1.1k
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(Closed) LoopSeq synthetic long reads technology
... Hi everyone, I was wondering if anyone has had experience with [LoopSeq][1]? It's a prep-kit to produce synthetic amplicon long reads using Illumina sequencers. Thoughts on performance? Any ideas on the principle of the technology? There's not much information on the technology out there. [1] ...
loop synthetic long reads written 27 days ago by BioinformaticsBro10
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Comment: C: Fields with biggest demand for bioinformatics?
... So more CS than biology. Makes sense, since that applies in general as well. ...
written 29 days ago by BioinformaticsBro10
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Comment: C: Fields with biggest demand for bioinformatics?
... Hi, I've gotten into bioinformatics recently and am currently exploring what fields to go deep into. The impression of the shortage comes from other biologists mostly, but an anecdote isn't data so I'm hoping to find some research to confirm/deny this. As for interest, I've started looking into bact ...
written 29 days ago by BioinformaticsBro10
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Forum: Fields with biggest demand for bioinformatics?
... As the title suggest, what are the fields with the biggest demand for bioinformaticists? There's pretty much a shortage of experienced bioinformatcists in every field but which ones are hardest hit? Proteomics? Transcriptomics? Pharmocogenetics? Has there been any research on this question? ...
career forum written 29 days ago by BioinformaticsBro10 • updated 29 days ago by Jean-Karim Heriche18k
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Comment: C: Shotgun metagenomics: Why bother with de novo assembly?
... All valid points! I forgot about the extra resolution that can be gained from contigs vs. reads alone. This does raise some other thoughts. You would generally get longer contigs from abundant species. Long contigs leads to better resolution. Thus, abundant species would be profiled better. In the ...
written 4 weeks ago by BioinformaticsBro10
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Shotgun metagenomics: Why bother with de novo assembly?
... Hi everyone, I've started learning about shotgun metagenomics sequencing. My understanding is there are two main approaches: mapping-based and assembly-based. In the former, you simply map reads to a database to determine classification and perform some type of functional profiling. In the latter, y ...
assembly metagnomics written 4 weeks ago by BioinformaticsBro10

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