User: Devon Ryan

gravatar for Devon Ryan
Devon Ryan1.9k
Reputation:
1,920
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Location:
Germany
Twitter:
dpryan79
Last seen:
3 weeks, 2 days ago
Joined:
3 years, 5 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 • 345 results • page 1 of 35 • next >
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Answer: A: deepTools2: compute matrix error
... Your problem is caused by mixing wormbase chromosome names (`CHROMOSOME_I`, `CHROMOSOME_II`, etc.) with UCSC chromosome names (`chrI`, `chrII`). We wrote deepTools to be able to translate between some chromosome naming systems, but wormbase is weird enough that I never wrote code to support translat ...
written 26 days ago by Devon Ryan1.9k
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Comment: C: deepTools2: compute matrix error
... If you share that history with "ryan@ie-freiburg.mpg.de" I'll have a look at why that's happening. ...
written 26 days ago by Devon Ryan1.9k
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Comment: C: deepTools2: compute matrix error
... Usually this happens if the BED or GTF file doesn't actually match the bigWig files you're using (e.g., they're from different organisms). Are you using usegalaxy.org? ...
written 26 days ago by Devon Ryan1.9k
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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 11 weeks 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 4 months 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 months 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 4 months 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 4 months ago by Devon Ryan1.9k
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Comment: C: Lock screen pink
... You're on the wrong site :) ...
written 4 months 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 5 months ago by Devon Ryan1.9k

Latest awards to Devon Ryan

Scholar 4 months ago, created an answer that has been accepted. For A: Docker Galaxy Job conf file and SLURM
Scholar 8 months ago, created an answer that has been accepted. For A: Docker Galaxy Job conf file and SLURM
Teacher 8 months ago, created an answer with at least 3 up-votes. For C: Galaxy Tool Unit Test
Scholar 9 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: Docker Galaxy Job conf file and SLURM
Scholar 16 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
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Scholar 20 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Teacher 20 months ago, created an answer with at least 3 up-votes. For C: Galaxy Tool Unit Test
Teacher 20 months ago, created an answer with at least 3 up-votes. For C: Galaxy Tool Unit Test
Scholar 20 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
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Scholar 23 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Unicode error after installing package_python_2_7_10
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Unicode error after installing package_python_2_7_10
Scholar 23 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Scholar 23 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Scholar 23 months ago, created an answer that has been accepted. For A: Specificy runner to use per tool
Scholar 23 months ago, created an answer that has been accepted. For C: gtf file error
Scholar 24 months ago, created an answer that has been accepted. For C: gtf file error
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Scholar 2.1 years ago, created an answer that has been accepted. For A: Unicode error after installing package_python_2_7_10
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