Admin: Devon Ryan

gravatar for Devon Ryan
Devon Ryan85k
Reputation:
84,820
Status:
Trusted
Location:
Freiburg, Germany
Twitter:
dpryan79
Scholar ID:
Google Scholar Page
Last seen:
1 day, 8 hours ago
Joined:
5 years, 7 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 • 9,642 results • page 1 of 965 • next >
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Comment: C: Merging fastq files
... Not if they're the same library. If a different library was made then quite likely (less so if they use a robot for library prep). ...
written 1 day ago by Devon Ryan85k
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Comment: C: Deeptools plotCorrelation function bug?
... Which version are you using? There was indeed a few versions where the labels were in the wrong order. ...
written 1 day ago by Devon Ryan85k
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Comment: C: Merging fastq files
... Give us more details about not being able to `cat` the files together. That should almost always work. BTW, point out to your boss that we can determine the number of runs from looking at the fastq files, so it's not like concatenating the files is really going to mask that from reviewers that care ...
written 1 day ago by Devon Ryan85k
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Comment: C: How to run eXpress RNA-seq quantification?
... Benchmarking results aren't going to change for a different disease area unless you have something really weird going on, like VDJ recombination. ...
written 4 days ago by Devon Ryan85k
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Comment: C: How to run eXpress RNA-seq quantification?
... There have been a lot of benchmarking papers out there, is there a reason you want to perform yet another benchmark? ...
written 4 days ago by Devon Ryan85k
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Answer: A: How is it possible to have more than 25000 genes in counts file?
... Not all genes are protein coding. ...
written 4 days ago by Devon Ryan85k
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Comment: C: Mapping query sequence with RNA-Seq
... As in less than 100% align or none of the reads align perfectly? ...
written 4 days ago by Devon Ryan85k
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Comment: C: Acceptable duplication levels in ATAC-Seq data
... Yeah, human or mouse. For super small genomes like yeast I would expect higher duplication rates like you're observing. ...
written 5 days ago by Devon Ryan85k
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Comment: C: How to write the output in snakefile (snakemake) for bowtie2-build
... See if those files show up eventually. We usually use `--latency-wait 300` do get around this. ...
written 5 days ago by Devon Ryan85k
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Answer: A: Acceptable duplication levels in ATAC-Seq data
... This will end up varying strongly based upon your sequencing depth, which is why there aren't any strict thresholds. If you're looking at differential accessibility then the most important thing is that you have comparable duplication rates across samples/groups. For what it's worth, our most recent ...
written 5 days ago by Devon Ryan85k

Latest awards to Devon Ryan

Teacher 1 day ago, created an answer with at least 3 up-votes. For A: Normalizing Rna-Seq Data Using Ercc Spike-In
Commentator 2 days ago, created a comment with at least 3 up-votes. For C: Bwa Mem Method For Mapping, With Or Without Trimming Reads?
Good Answer 3 days ago, created an answer that was upvoted at least 5 times. For C: Error at the end of HT-seq Analysis and output.txt with 0 bytes in size
Appreciated 3 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Normalizing Rna-Seq Data Using Ercc Spike-In
Good Answer 4 days ago, created an answer that was upvoted at least 5 times. For C: Error at the end of HT-seq Analysis and output.txt with 0 bytes in size
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Where Is Mirna Binding Site On Mrna ?
Appreciated 10 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Great Question 15 days ago, created a question with more than 5,000 views. For Is There A Faster Replacement For Fastq-Dump (From The Sra-Toolkit)?
Scholar 15 days ago, created an answer that has been accepted. For A: deepTools2: compute matrix error
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: Where Is Mirna Binding Site On Mrna ?
Good Answer 16 days ago, created an answer that was upvoted at least 5 times. For C: Error at the end of HT-seq Analysis and output.txt with 0 bytes in size
Appreciated 16 days ago, created a post with more than 5 votes. For Replace me: bioinformatician/post-doc at the DZNE (Bonn, Germany)
Appreciated 16 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Good Answer 16 days ago, created an answer that was upvoted at least 5 times. For C: Error at the end of HT-seq Analysis and output.txt with 0 bytes in size
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: Where Is Mirna Binding Site On Mrna ?
Scholar 17 days ago, created an answer that has been accepted. For A: deepTools2: compute matrix error
Scholar 18 days ago, created an answer that has been accepted. For A: De-multiplex of no illumina index RNAseq libraries on Novaseq
Scholar 18 days ago, created an answer that has been accepted. For A: logCPM to RPKM
Scholar 18 days ago, created an answer that has been accepted. For A: deepTools2: compute matrix error
Scholar 19 days ago, created an answer that has been accepted. For A: deepTools2: compute matrix error
Good Answer 20 days ago, created an answer that was upvoted at least 5 times. For C: Error at the end of HT-seq Analysis and output.txt with 0 bytes in size
Teacher 23 days ago, created an answer with at least 3 up-votes. For A: Where Is Mirna Binding Site On Mrna ?
Scholar 23 days ago, created an answer that has been accepted. For A: deepTools2: compute matrix error
Appreciated 24 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs

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