User: Devon Ryan

gravatar for Devon Ryan
Devon Ryan1.9k
Reputation:
1,910
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Trusted
Location:
Germany
Twitter:
dpryan79
Last seen:
3 days ago
Joined:
3 years, 1 month 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 • 341 results • page 1 of 35 • next >
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Comment: C: Featurecounts for paired end RNA-seq reads not generating counts
... How big is the file? ...
written 3 days 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 4 days 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 12 days 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 19 days ago by Devon Ryan1.9k
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Comment: C: Lock screen pink
... You're on the wrong site :) ...
written 23 days 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 4 weeks 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 7 weeks 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 7 weeks 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 7 weeks ago by Devon Ryan1.9k
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Comment: C: interval file to fastq conversiosn
... Post a line or two of the interval file. ...
written 3 months ago by Devon Ryan1.9k

Latest awards to Devon Ryan

Scholar 12 days ago, created an answer that has been accepted. For A: Docker Galaxy Job conf file and SLURM
Scholar 4 months ago, created an answer that has been accepted. For A: Docker Galaxy Job conf file and SLURM
Teacher 4 months ago, created an answer with at least 3 up-votes. For C: Galaxy Tool Unit Test
Scholar 5 months ago, created an answer that has been accepted. For A: Docker Galaxy Job conf file and SLURM
Scholar 10 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: Sub groups within galaxy shed tool conf file
Scholar 13 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Scholar 16 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Teacher 16 months ago, created an answer with at least 3 up-votes. For C: Galaxy Tool Unit Test
Teacher 16 months ago, created an answer with at least 3 up-votes. For C: Galaxy Tool Unit Test
Scholar 16 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Guru 17 months ago, received more than 100 upvotes.
Supporter 18 months ago, voted at least 25 times.
Scholar 19 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Unicode error after installing package_python_2_7_10
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Unicode error after installing package_python_2_7_10
Scholar 19 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Scholar 19 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Scholar 19 months ago, created an answer that has been accepted. For A: Specificy runner to use per tool
Scholar 19 months ago, created an answer that has been accepted. For C: gtf file error
Scholar 20 months ago, created an answer that has been accepted. For C: gtf file error
Scholar 20 months ago, created an answer that has been accepted. For C: gtf file error
Centurion 20 months ago, created 100 posts.
Scholar 21 months ago, created an answer that has been accepted. For A: Unicode error after installing package_python_2_7_10
Scholar 22 months ago, created an answer that has been accepted. For A: Unicode error after installing package_python_2_7_10

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