User: Devon Ryan

gravatar for Devon Ryan
Devon Ryan1.9k
Reputation:
1,870
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Location:
Germany
Twitter:
dpryan79
Last seen:
1 day, 7 hours ago
Joined:
3 years 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 • 336 results • page 2 of 34 • next >
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Answer: A: Can we map fastq files with paired ends using bwa mem on galaxy?
... Yes, bwa-mem can take a paired-end collection. ...
written 3 months ago by Devon Ryan1.9k
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Comment: C: Why the GFF file doesn't have any exons in anotation?
... Where did you get the file from? ...
written 3 months ago by Devon Ryan1.9k
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Comment: C: Problem with dependencies: Conda/freebayes
... Have you tried just reinstalling it? ...
written 3 months ago by Devon Ryan1.9k
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Comment: C: How to create GFF file for HT seq
... Please post new questions as new posts in the future and not as answers to old posts. As the first warning indicates, you don't have any exons in your annotation. I have no idea how that happened, but you'll need to figure it out. ...
written 3 months ago by Devon Ryan1.9k
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Comment: C: How to do the peak calling with "MACS2 bdgbroadcall" for H3K9me3 ChIP-seq
... MACS2 has a `--broad` option (this is the "Advanced Option" -> "Composite broad regions" -> "broad regions" option in Galaxy). I strongly encourage you not to directly run `bdgbroadcall` at any point, instead simply use `MACS2 callpeak`. The various `bdg*` programs are run internally by `callp ...
written 4 months ago by Devon Ryan1.9k
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Answer: A: Ensembl numbers to gene symbols
... Text works just fine, you'll just want to ensure that it's set as the "tabular" datatype in Galaxy. ...
written 4 months ago by Devon Ryan1.9k
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Answer: A: Changing file_path to local database/files directory
... 1. All files stored by Galaxy are called something like `dataset_XXXX.dat`, where `XXXX` is a number. Eventually you'll find many directories of these. Uploaded files should go elsewhere and Galaxy can then be configured to know where they are. 2. No, the ftp server should create folders with your u ...
written 4 months ago by Devon Ryan1.9k
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Comment: C: Docker Galaxy Job conf file and SLURM
... Add something like `-n 4` to the . That'll make everything default to 4 cores. ...
written 4 months ago by Devon Ryan1.9k
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Comment: C: RNA-Seq Alignment too Big for Galaxy?
... Those aren't too big. Are you running this on usegalaxy.org or a different Galaxy server? ...
written 4 months ago by Devon Ryan1.9k
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Comment: C: Docker Galaxy Job conf file and SLURM
... Are you using the default `slurm` job runner or have you already changed something in `job_conf.xml`? ...
written 4 months ago by Devon Ryan1.9k

Latest awards to Devon Ryan

Scholar 3 months ago, created an answer that has been accepted. For A: Docker Galaxy Job conf file and SLURM
Teacher 3 months ago, created an answer with at least 3 up-votes. For C: Galaxy Tool Unit Test
Scholar 4 months ago, created an answer that has been accepted. For A: Docker Galaxy Job conf file and SLURM
Scholar 9 months ago, created an answer that has been accepted. For A: Docker Galaxy Job conf file and SLURM
Scholar 11 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Scholar 12 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Teacher 15 months ago, created an answer with at least 3 up-votes. For C: Galaxy Tool Unit Test
Scholar 15 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Teacher 15 months ago, created an answer with at least 3 up-votes. For C: Galaxy Tool Unit Test
Scholar 15 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Guru 16 months ago, received more than 100 upvotes.
Supporter 17 months ago, voted at least 25 times.
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 A: Unicode error after installing package_python_2_7_10
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Unicode error after installing package_python_2_7_10
Scholar 18 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: Specificy runner to use per tool
Scholar 18 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 C: gtf file error
Scholar 19 months ago, created an answer that has been accepted. For C: gtf file error
Scholar 19 months ago, created an answer that has been accepted. For C: gtf file error
Centurion 19 months ago, created 100 posts.
Scholar 20 months ago, created an answer that has been accepted. For A: Unicode error after installing package_python_2_7_10
Scholar 21 months ago, created an answer that has been accepted. 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

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