Admin: Devon Ryan

gravatar for Devon Ryan
Devon Ryan91k
Reputation:
91,220
Status:
Trusted
Location:
Freiburg, Germany
Twitter:
dpryan79
Scholar ID:
Google Scholar Page
Last seen:
13 minutes ago
Joined:
6 years, 5 months ago
Email:
d*******@gmail.com

I'm currently a bioinformatician/data manager at the Max Planck Institute for Immunobiology and Epigenetics in Freiburg, Germany.

I was a post-doc at the DZNE in Bonn, Germany, spending much of my time working on epigenetics and NGS.

Posts by Devon Ryan

<prev • 10,075 results • page 2 of 1008 • next >
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Comment: C: Looking for Participants: Meenta NovaSeq RunShare Beta
... I guess that's their hope. We'll see what happens. ...
written 4 weeks ago by Devon Ryan91k
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Comment: C: Looking for Participants: Meenta NovaSeq RunShare Beta
... Why would someone want to do this rather than send samples to a company/core and have them do the work of ensuring the flow cells are filled? ...
written 4 weeks ago by Devon Ryan91k
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Comment: C: Processing .raw files or out.tar files from Mass Spec
... The raw output is specific to each manufacturer and can usually only be handled on Windows. The only software I know of that can handle some raw output files on anything other than windows is maxquant, which works with at least some thermo fisher raw data. ...
written 4 weeks ago by Devon Ryan91k
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Comment: C: Should I generate a new Index genome in STAR for 50 base reads instead of 100 ba
... The quote from the manual contradicts that recalculating the STAR index is likely to be very useful. ...
written 5 weeks ago by Devon Ryan91k
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Comment: C: WGBS alignment with BitMapperBS
... I have to admit being surprised by how fast bitmapperBS is. For those wondering you can install it via conda. ...
written 5 weeks ago by Devon Ryan91k
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Comment: C: missingoutputexception, snakemake after completing 95% analysis
... Happens to all of us :) ...
written 5 weeks ago by Devon Ryan91k
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Comment: C: HIsat2 bam and summary output - multiple output file type
... Isn't that printed to `stderr`? So just redirect that to a new file. ...
written 5 weeks ago by Devon Ryan91k
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Comment: C: missingoutputexception, snakemake after completing 95% analysis
... It's likely that there's a typo in the the output file name. Just double check that. ...
written 5 weeks ago by Devon Ryan91k
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Comment: C: Samtools problem with running (Conda)
... I assume you mean a dedicated environment, since a dedicated conda installation would be rather wasteful. ...
written 6 weeks ago by Devon Ryan91k
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Comment: C: salmon NumReads inconsistent with depth from --writeMappings?
... What I think you're observing is a result of the default ~8000 depth in `samtools depth` and `samtools mpileup`. In essence, this is the size of a buffer for holding reads and once the depth goes much above this you're going to start seeing some odd behavior due to that (I don't recall the details o ...
written 6 weeks ago by Devon Ryan91k

Latest awards to Devon Ryan

Teacher 3 days ago, created an answer with at least 3 up-votes. For A: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: How To Download The Entire Human Gene List With Their Chromosomal Location
Appreciated 6 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Concatenate Two .Fasta Files Into One
Good Answer 22 days ago, created an answer that was upvoted at least 5 times. For A: How To Download The Entire Human Gene List With Their Chromosomal Location
Appreciated 25 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: How To Download The Entire Human Gene List With Their Chromosomal Location
Popular Question 5 weeks ago, created a question with more than 1,000 views. For BWA 0.7.11 is out, supports ALT contigs
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: How To Download The Entire Human Gene List With Their Chromosomal Location
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: How To Download The Entire Human Gene List With Their Chromosomal Location
Appreciated 6 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How To Download The Entire Human Gene List With Their Chromosomal Location
Appreciated 6 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: Bwa Mem Method For Mapping, With Or Without Trimming Reads?
Good Answer 7 weeks ago, created an answer that was upvoted at least 5 times. For A: How To Download The Entire Human Gene List With Their Chromosomal Location
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Appreciated 8 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Scholar 8 weeks ago, created an answer that has been accepted. For A: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: Bwa Mem Method For Mapping, With Or Without Trimming Reads?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Popular Question 9 weeks ago, created a question with more than 1,000 views. For BWA 0.7.11 is out, supports ALT contigs
Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: Intersection of multiple methods for RNA-Seq differential expression: conservati
Appreciated 10 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs

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