User: Devon Ryan

gravatar for Devon Ryan
Devon Ryan1.9k
Reputation:
1,910
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Trusted
Location:
Germany
Twitter:
dpryan79
Last seen:
8 minutes ago
Joined:
3 years, 3 months ago
Email:
d*******@gmail.com

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 • 342 results • page 1 of 35 • next >
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Comment: C: multiBamSummary in DeepTools_sample order did not match to the entry
... What version of `multiBamSummary` and `plotCorrelation` are you using? ...
written 18 days ago by Devon Ryan1.9k
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Comment: C: Featurecounts for paired end RNA-seq reads not generating counts
... How big is the file? ...
written 8 weeks ago by Devon Ryan1.9k
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Comment: C: Featurecounts for paired end RNA-seq reads not generating counts
... It's likely that the GFF (try to find a GTF file, they tend to work better) didn't match your genome version. To check this, load both a BAM file and your GFF file in IGV and spot check a few genes too see if the lack of counts is reasonable. ...
written 8 weeks ago by Devon Ryan1.9k
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Answer: A: Why gene counts from RNA STAR don't match total uniquely mapped counts
... Many alignments in your dataset aren't to genes, but rather intronic or intergenic regions. Those can't be in the counts but can still align uniquely. ...
written 10 weeks ago by Devon Ryan1.9k
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Answer: A: Extracting Gene Names from BigWig File
... You have a couple options. Firstly, diffBind is a standard tool for looking at differential binding. If you don't need p-values, it can be helpful to put your bigWig files into computeMatrix and then plotHeatmap. In plotHeatmap, you can perform k-means clustering to find clusters with more signal in ...
written 11 weeks ago by Devon Ryan1.9k
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Comment: C: Lock screen pink
... You're on the wrong site :) ...
written 11 weeks ago by Devon Ryan1.9k
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Comment: C: Running DESeq2 inside local Galaxy instance
... Odd, I suspect that there was an error when creating the conda environment. You can try removing it (as the galaxy user on the command line) and reinstalling it (preferably via Galaxy). Worst case scenario, one of us can give you our `environment.yaml`. ...
written 3 months ago by Devon Ryan1.9k
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Comment: C: Incorrect dependencies used during job run
... `cd` into one of the job working directories and look at the tool script. It will have a section where it activates the various environments. Run that as the galaxy user, run `hash -r` and then `which samtools`. My guess is that for some reason one or more of the conda packages didn't get installed ...
written 3 months ago by Devon Ryan1.9k
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Comment: C: inquiry about the analysis of a dominant mutant with GALAXY
... You'll need to specify which particular tools in Galaxy you're using, specifically which one you're using to produce the plot you mention. ...
written 3 months ago by Devon Ryan1.9k
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Comment: C: safari can't connect to the server "localhost".
... Did you restart Galaxy after changing the settings? If yes, check the error logs. ...
written 3 months ago by Devon Ryan1.9k

Latest awards to Devon Ryan

Scholar 10 weeks ago, created an answer that has been accepted. For A: Docker Galaxy Job conf file and SLURM
Scholar 6 months ago, created an answer that has been accepted. For A: Docker Galaxy Job conf file and SLURM
Teacher 6 months ago, created an answer with at least 3 up-votes. For C: Galaxy Tool Unit Test
Scholar 7 months ago, created an answer that has been accepted. For A: Docker Galaxy Job conf file and SLURM
Scholar 12 months ago, created an answer that has been accepted. For A: Docker Galaxy Job conf file and SLURM
Scholar 14 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Scholar 14 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Scholar 18 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Teacher 18 months ago, created an answer with at least 3 up-votes. For C: Galaxy Tool Unit Test
Teacher 18 months ago, created an answer with at least 3 up-votes. For C: Galaxy Tool Unit Test
Scholar 18 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Guru 19 months ago, received more than 100 upvotes.
Supporter 20 months ago, voted at least 25 times.
Scholar 21 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Unicode error after installing package_python_2_7_10
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Unicode error after installing package_python_2_7_10
Scholar 21 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Scholar 21 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Scholar 21 months ago, created an answer that has been accepted. For A: Specificy runner to use per tool
Scholar 21 months ago, created an answer that has been accepted. For C: gtf file error
Scholar 21 months ago, created an answer that has been accepted. For C: gtf file error
Scholar 22 months ago, created an answer that has been accepted. For C: gtf file error
Centurion 22 months ago, created 100 posts.
Scholar 23 months ago, created an answer that has been accepted. For A: Unicode error after installing package_python_2_7_10
Scholar 24 months ago, created an answer that has been accepted. For A: Unicode error after installing package_python_2_7_10

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