User: Devon Ryan

gravatar for Devon Ryan
Devon Ryan1.9k
Reputation:
1,850
Status:
Trusted
Location:
Germany
Twitter:
dpryan79
Last seen:
3 hours ago
Joined:
2 years, 9 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 • 329 results • page 1 of 33 • next >
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Answer: C: Problem with dependencies: Conda/freebayes
... Can you manually create the `__parallel@20170422` conda environment (it should have parallel-20170422 and perl-5.22.0.1)? I'm also running 17.09 and this all installed OK on my instance via conda. What may be happening is that conda is having trouble resolving a dependency for some odd reason (this ...
written 8 days ago by Devon Ryan1.9k
0
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Answer: C: Why does my GFF3 file not have any exons in the annotation lines read by HTseq-c
... Yes, it's missing exons. You should ask the authors why this is, since that's quite annoying. ...
written 9 days ago by Devon Ryan1.9k
1
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Comment: C: what i can do with this error
... Please post the actual error message. ...
written 9 days ago by Devon Ryan1.9k
1
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1
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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 9 days ago by Devon Ryan1.9k
0
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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 10 days ago by Devon Ryan1.9k
0
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Comment: C: Problem with dependencies: Conda/freebayes
... Have you tried just reinstalling it? ...
written 12 days ago by Devon Ryan1.9k
0
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6
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6
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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 12 days ago by Devon Ryan1.9k
2
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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 25 days ago by Devon Ryan1.9k
1
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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 weeks ago by Devon Ryan1.9k
2
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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 5 weeks ago by Devon Ryan1.9k

Latest awards to Devon Ryan

Scholar 5 days ago, created an answer that has been accepted. For A: Docker Galaxy Job conf file and SLURM
Teacher 5 days ago, created an answer with at least 3 up-votes. For C: Galaxy Tool Unit Test
Scholar 4 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
Scholar 8 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Scholar 8 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Teacher 11 months ago, created an answer with at least 3 up-votes. For C: Galaxy Tool Unit Test
Scholar 11 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Teacher 11 months ago, created an answer with at least 3 up-votes. For C: Galaxy Tool Unit Test
Scholar 12 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
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Scholar 15 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
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Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Unicode error after installing package_python_2_7_10
Scholar 15 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Scholar 15 months ago, created an answer that has been accepted. For A: Specificy runner to use per tool
Scholar 15 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Scholar 15 months ago, created an answer that has been accepted. For C: gtf file error
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Scholar 17 months ago, created an answer that has been accepted. For A: Unicode error after installing package_python_2_7_10
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