User: Devon Ryan

gravatar for Devon Ryan
Devon Ryan1.4k
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Germany
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dpryan79
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8 hours ago
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Bioinformatician / data manager at the Max Planck Institute for Immunobiology and Epigenetics in Freiburg, Germany. I'm one of the developers for deepTools (among other packages).

Posts by Devon Ryan

<prev • 253 results • page 1 of 26 • next >
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Comment: C: normalisation between different ChIP-seq data
... You'll have to install diffBind in R and download the BAM files and überpeaks from Galaxy. ...
written 22 hours ago by Devon Ryan1.4k
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Comment: C: normalisation between different ChIP-seq data
... What's the end goal? I suspect that you might like to use `computeMatrix` and `plotHeatmap` from deepTools to help generate some hypotheses before moving on to using something like diffbind. As an aside, you'll have better luck at the moment using diffBind locally and just downloading the files fro ...
written 1 day ago by Devon Ryan1.4k
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Answer: C: TopHat Error stating that (installed) Bowtie2 is not installed
... 1. Have a look for an `env.sh` file in a tophat directory under `tool_deps/`, sometimes those go missing. 2. Switch to conda for dependency resolution, it makes life SO much easier. 3. Don't use tophat for any new analyses. STAR is the probably the best aligner to use and it works well in Galaxy. If ...
written 7 days ago by Devon Ryan1.4k
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Comment: C: DeepTools plot correlation image error
... Perhaps they'll record them. I know that was attempted last year and there were "issues" of some sort with it. We have the training material from last years session online (deeptools.ie-freiburg.mpg.de under "shared data" -> "data libraries" and "pages"), so perhaps have a quick browse through th ...
written 8 days ago by Devon Ryan1.4k
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Answer: A: DeepTools plot correlation image error
... As suspected, each bin has at least 1 NaN in it, so there's no way to plot a very reliable correlation. The root of this problem is how you used multiBigwigSummary. Your input only BED files that contained peaks, when what you really should have input are bigWig files made with `bamCoverage` direct ...
written 8 days ago by Devon Ryan1.4k
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Comment: C: How to create a Fasta file of mouse genome from download chromosome files
... 1. It only matters if you need to merge other datasets, since occasionally tools don't properly handle BAM files with different chromosome ordering. You can always reorder things with picard if this is ever an issue. 2. Sure, it's just slightly incomplete. 3. That sounds correct, telomeres are ha ...
written 8 days ago by Devon Ryan1.4k
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Answer: A: How to create a Fasta file of mouse genome from download chromosome files
... 1. All of them. 2. Contigs that have yet to be fully incorporated into chromosomes. With the exception of the `chrUn`s, the chromosome is known, but the exact location on them is not. 3. Contigs where the chromosome is unknown. Yes, include them. 4. ? 19 chromosomes plus sex chromosomes makes 20 ...
written 8 days ago by Devon Ryan1.4k
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Comment: C: DeepTools plot correlation image error
... BTW, I suspect that the input matrix had 24397 (or so) entries and that each of these contained an NaN in it. That's the most likely cause, but then that begs the question regarding how THAT happened. ...
written 9 days ago by Devon Ryan1.4k
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Comment: C: DeepTools plot correlation image error
... Can you share a history containing this and the input matrix with me (my account on usegalaxy.org is ryan@ie-freiburg.mpg.de)? I can then more easily have a look at this. ...
written 9 days ago by Devon Ryan1.4k
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Comment: C: Galaxy Installation fails
... What are the permissions in `/software/python/2.7.13/lib/python2.7/site-packages`? ...
written 11 days ago by Devon Ryan1.4k

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