Admin: Devon Ryan

gravatar for Devon Ryan
Devon Ryan89k
Reputation:
89,240
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Trusted
Location:
Freiburg, Germany
Twitter:
dpryan79
Scholar ID:
Google Scholar Page
Last seen:
10 hours ago
Joined:
6 years 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 • 9,965 results • page 2 of 997 • next >
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Answer: A: How much importance is RNAseq experimental bias?
... The difference in the number of pooled brains isn't a particular problem, though hopefully those were pooled from litter mates and then litters used as biological samples. What you should watch out for is if some brains took longer to extract and process than others, since that will certainly lead t ...
written 5 days ago by Devon Ryan89k
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Comment: C: Is there a way to compare single-cell RNA seq and Ribotag-seq?
... You'll have to think about what you really want to get out of the data. Most likely you'll want to look at how DE genes in your Ribotag data change in different cells in your scRNA-seq data (with only 60 cells, I expect you explicitly took different cell types). ...
written 5 days ago by Devon Ryan89k
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Answer: A: Why are lowly expressed genes less likely to detect as DE?
... The strength of fold change and variance shrinkage scales inversely with the size of the values (and the number of them). As a rule, power increases with sample number and the number of read counts per gene. ...
written 6 days ago by Devon Ryan89k
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Comment: C: Bwa Mem Have Different Alignment Result When Using Different Threads
... > something is either reproducible or not I think this is a common misconception about what reproducibility should really mean. The goal shouldn't be to get the exact same result, since that's not even possible by using deterministic software in a docker container on different systems. The goal ...
written 6 days ago by Devon Ryan89k
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Comment: C: GC content of 10x Genomics
... It will affect all kits and I suspect there is a GC bias at the 3' end (likely exacerbated by this being RNA-seq, so there are enrichments of a handful of sequences anyway). ...
written 6 days ago by Devon Ryan89k
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Comment: C: GC content of 10x Genomics
... I can't say I've looked at this specifically for 10X data, but in general FastQC reports for 3' RNA-seq datasets (single-cell like or the bulk stuff with a kit from Lexogen) tend to look rather odd. My suspicion has always been that this is due to the nature of the 3' end of transcripts. ...
written 7 days ago by Devon Ryan89k
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Comment: C: Distribute proportionality calculations on many nodes (SLURM)
... Is there a reason you haven't asked your cluster admin for the appropriate syntax for your cluster? ...
written 8 days ago by Devon Ryan89k
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Comment: C: Oases Makefile:114: recipe for target 'obj/oases.o' failed
... ![enter image description here][1] Really though, do you not have better things to do with your time? [1]: https://i.imgflip.com/2y46y6.jpg ...
written 9 days ago by Devon Ryan89k
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Comment: C: do paired end reads both mapped to the same gene appear consecutive to each othe
... `--reorder` is doing something different, it's ensuring that the order of the pairs matches what's in the fastq file, not that pairs themselves have any particular order. ...
written 10 days ago by Devon Ryan89k
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Answer: A: do paired end reads both mapped to the same gene appear consecutive to each othe
... Bowtie2, like most aligners, will always output paired-end reads in chunks where read #1 and its multimapping alignments comes first and then read #2 and its multimapping alignments comes next. That's usually easy enough to parse. If you need the primary and secondary alignment in a different order ...
written 10 days ago by Devon Ryan89k

Latest awards to Devon Ryan

Teacher 1 day ago, created an answer with at least 3 up-votes. For A: Distance Between Genes Of Interest
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: Distance Between Genes Of Interest
Scholar 6 days ago, created an answer that has been accepted. For A: How To Create A Bigwig File And Display It
Scholar 10 days ago, created an answer that has been accepted. For A: How To Create A Bigwig File And Display It
Commentator 10 days ago, created a comment with at least 3 up-votes. For C: Perl Script To Make Statistics Of Mirna Abundances For Many Samples
Good Answer 10 days ago, created an answer that was upvoted at least 5 times. For A: When should you use SVA vs. ComBat?
Appreciated 10 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Distance Between Genes Of Interest
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Distance Between Genes Of Interest
Appreciated 13 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: Distance Between Genes Of Interest
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: Distance Between Genes Of Interest
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: Distance Between Genes Of Interest
Scholar 16 days ago, created an answer that has been accepted. For A: Count antisense transcripts using STAR --quantMode
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: Distance Between Genes Of Interest
Teacher 24 days ago, created an answer with at least 3 up-votes. For A: Distance Between Genes Of Interest
Scholar 24 days ago, created an answer that has been accepted. For A: Count antisense transcripts using STAR --quantMode
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: When should you use SVA vs. ComBat?
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: When should you use SVA vs. ComBat?
Appreciated 5 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Appreciated 6 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Appreciated 6 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs

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