User: Devon Ryan

gravatar for Devon Ryan
Devon Ryan1.5k
Reputation:
1,500
Status:
Trusted
Location:
Germany
Twitter:
dpryan79
Last seen:
13 hours ago
Joined:
2 years, 2 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 • 270 results • page 1 of 27 • next >
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Comment: C: file format conversion
... Right, but what's in it? ...
written 7 days ago by Devon Ryan1.5k
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Comment: C: file format conversion
... What are the first 10 or so of the uncompressed lines? `bz2` is a compression format, `.txt` can be anything and might already be fastq. ...
written 8 days ago by Devon Ryan1.5k
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Comment: C: cufflinks on Rna -seq data not working
... It takes a fair bit of time, but at least for me cufflinks jobs do start on usegalaxy.org ...
written 10 days ago by Devon Ryan1.5k
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Comment: C: Analyzing ChIP-seq data from HiSeq 3000
... Those are great metrics, your alignment went fine. Have you run `plotFingerprint` on these samples? Perhaps your IP is bad. ...
written 11 days ago by Devon Ryan1.5k
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Answer: C: ERROR WHEN RUNNING AN RNA STYAR ANALYSIS
... This isn't something you can change, the Galaxy admins are still trying to optimize the RAM settings for STAR. ...
written 11 days ago by Devon Ryan1.5k
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Answer: A: Analyzing ChIP-seq data from HiSeq 3000
... Fastq files produced by a HiSeq 3000 are no different from those produced by any other HiSeq in the last ~5 years. Perhaps you need to trim your data a bit or you have significant contamination (e.g., from Wolbachia). What sort of alignment metrics are you getting? ...
written 11 days ago by Devon Ryan1.5k
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Answer: A: Tophat is not anymore among the galaxy tools
... Please [see here](https://biostar.usegalaxy.org/p/23367/). In short, switch to hisat2 or STAR (the indices aren't ready yet, so you have to provide a fasta file). ...
written 23 days ago by Devon Ryan1.5k
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Comment: C: How to convert .txt files into fastq file format
... Already fastq then, just change the datatype. ...
written 25 days ago by Devon Ryan1.5k
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Answer: C: How to convert .txt files into fastq file format
... It's likely that you just need to change the datatype attribute in the history item. Can you post the first 5-10 lines of one of the files though so we can be sure? ...
written 26 days ago by Devon Ryan1.5k
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Answer: A: how i can install tool from galaxy shed to galaxy
... If you don't know then you're not one. Find out who runs the Galaxy server you're using and ask them to install the tool. This isn't something you can do. ...
written 27 days ago by Devon Ryan1.5k

Latest awards to Devon Ryan

Scholar 5 weeks ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Scholar 8 weeks ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Scholar 5 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Teacher 5 months ago, created an answer with at least 3 up-votes. For C: Galaxy Tool Unit Test
Teacher 5 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: Sub groups within galaxy shed tool conf file
Guru 6 months ago, received more than 100 upvotes.
Supporter 7 months ago, voted at least 25 times.
Scholar 8 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Unicode error after installing package_python_2_7_10
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Unicode error after installing package_python_2_7_10
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: Specificy runner to use per tool
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 C: gtf file error
Scholar 8 months ago, created an answer that has been accepted. For C: gtf file error
Scholar 9 months ago, created an answer that has been accepted. For C: gtf file error
Centurion 9 months ago, created 100 posts.
Scholar 10 months ago, created an answer that has been accepted. For A: Unicode error after installing package_python_2_7_10
Scholar 11 months ago, created an answer that has been accepted. For A: Unicode error after installing package_python_2_7_10
Teacher 11 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
Appreciated 18 months ago, created a post with more than 5 votes. For A: looking for a tool
Scholar 18 months ago, created an answer that has been accepted. 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

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