User: Devon Ryan

gravatar for Devon Ryan
Devon Ryan1.6k
Reputation:
1,630
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Location:
Germany
Twitter:
dpryan79
Last seen:
12 hours ago
Joined:
2 years, 4 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 • 293 results • page 1 of 30 • next >
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Answer: A: Help with sorting and merging two biological replicate bam file?
... In Galaxy, bowtie2 will return a sorted BAM file. If you need to merge BAM files you can use the "Merge BAM Files" tool under "NGS: SAMtools". ...
written 4 days ago by Devon Ryan1.6k
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Answer: A: How to get raw reads from bam file
... You'll want to use `featureCounts`, which is available in Galaxy. You'll need to provide it with your BAM file and an annotation in GTF format so it knows where your genes/exons are. ...
written 4 days ago by Devon Ryan1.6k
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Comment: C: RNA-Seq analysis for 2 genes
... It'd make sense to quantify transcripts with something like salmon and then look for isoform switching in DESeq2. That or using DEXseq should presumably work. ...
written 4 days ago by Devon Ryan1.6k
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Comment: C: Running Galaxy on a 64 CPU Core, 512 Gig RAM Server
... I guess I just didn't run into many problems, just with the python environment (largely solved with the introduction of conda) and ensuring the file system was shared. ...
written 12 days ago by Devon Ryan1.6k
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Answer: A: Running Galaxy on a 64 CPU Core, 512 Gig RAM Server
... I'd work more to get Galaxy to just use your cluster (ours uses our slurm cluster), that's a better long-term solution. You don't need to use a resource manager for a single server, what you likely need to do is (A) increase the number of concurrent jobs that can run per user (B) increase the numbe ...
written 13 days ago by Devon Ryan1.6k
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Answer: A: RNA-Seq analysis for 2 genes
... If you only care about 2 genes it would have been vastly cheaper and faster to do qPCR. Anyway, yes, you must align the data to the entire genome (or transcriptome). You're better off with featureCounts and DEseq2 rather than cuff-anything. Analyse all of the genes but if you only care about 2 gene ...
written 16 days ago by Devon Ryan1.6k
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Comment: C: How to manually delete a galaxy user?
... Why not just purge the user in the Galaxy interface? The kilobyte or so of database space is negligible then. ...
written 29 days ago by Devon Ryan1.6k
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Comment: C: Poor overall alignment rates
... It's smallRNA-seq, so make sure you trim the reads. ...
written 4 weeks ago by Devon Ryan1.6k
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Answer: A: scripts written in-house
... Yes, "scripts written in-house" means some program that they wrote and haven't shared with anyone. ...
written 4 weeks ago by Devon Ryan1.6k
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Comment: C: Error installing own tool on a Galaxy Docker instance
... It'd be appreciated if you could post what the solution was, since that will help others with similar problems who come here via google. ...
written 5 weeks ago by Devon Ryan1.6k

Latest awards to Devon Ryan

Scholar 6 weeks ago, created an answer that has been accepted. For A: Docker Galaxy Job conf file and SLURM
Scholar 3 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Scholar 3 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Teacher 6 months ago, created an answer with at least 3 up-votes. For C: Galaxy Tool Unit Test
Scholar 6 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Teacher 7 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: Sub groups within galaxy shed tool conf file
Guru 8 months ago, received more than 100 upvotes.
Supporter 9 months ago, voted at least 25 times.
Scholar 10 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Unicode error after installing package_python_2_7_10
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Unicode error after installing package_python_2_7_10
Scholar 10 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Scholar 10 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Scholar 10 months ago, created an answer that has been accepted. For A: Specificy runner to use per tool
Scholar 10 months ago, created an answer that has been accepted. For C: gtf file error
Scholar 10 months ago, created an answer that has been accepted. For C: gtf file error
Scholar 10 months ago, created an answer that has been accepted. For C: gtf file error
Centurion 11 months ago, created 100 posts.
Scholar 12 months ago, created an answer that has been accepted. For A: Unicode error after installing package_python_2_7_10
Scholar 13 months ago, created an answer that has been accepted. For A: Unicode error after installing package_python_2_7_10
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Unicode error after installing package_python_2_7_10
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Unicode error after installing package_python_2_7_10
Appreciated 20 months ago, created a post with more than 5 votes. For A: looking for a tool
Scholar 20 months ago, created an answer that has been accepted. For A: Unicode error after installing package_python_2_7_10

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