Admin: Devon Ryan

gravatar for Devon Ryan
Devon Ryan73k
Reputation:
73,460
Status:
Trusted
Location:
Freiburg, Germany
Twitter:
dpryan79
Scholar ID:
Google Scholar Page
Last seen:
3 hours ago
Joined:
4 years, 8 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

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Answer: A: How to compare compare two Sam files to check mapping
... I happened to [write something a while back](https://github.com/dpryan79/Misc/blob/master/CompareBAMs.c) to compare equivalently sorted files from different aligners (or with different settings, or with/without post-processing) to see which alignments differ and why. It currently compares chromosome ...
written 3 hours ago by Devon Ryan73k
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Answer: A: how to draw two different Y-axes with deeptools?
... I think you posted this to the deepTools google-group too. But regardless, there's no way to do this directly in deepTools. I suggest that you export the data (there's an option for that in plotProfile) and then tweak things to your liking in R. ...
written 1 day ago by Devon Ryan73k
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Comment: C: Computer specs for Bioinformatics
... At least in our case anything important is on a separate (backed up!) storage array that's also used (in part) by the cluster. Then there's no reason to bother with RAID. ...
written 1 day ago by Devon Ryan73k
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Answer: A: Computer specs for Bioinformatics
... A bit more RAM never hurts, but if you just need this for small apps and test scripts then what you've already listed should suffice (for reference, my desktop has a similar use and it's a Dell Optiplex 9020). If you normally process files on a cluster then I assume you can get access to that file ...
written 1 day ago by Devon Ryan73k
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Comment: C: Biological significance of Fold_enrichment in macs2
... What do you think it means? ...
written 1 day ago by Devon Ryan73k
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Comment: C: plotProfile (deepTools) generated a peak on gene body region
... If you want to actually edit the heatmap then don't bother with `--outFileNameMatrix`, just `gunzip` the output from `computeMatrix`, remove the problematic line, change the `group_boundaries` so they limits are correct, and then gzip the results back up. In general, it's probably simpler to just f ...
written 1 day ago by Devon Ryan73k
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Comment: C: error bar in bar plot ggplot2
... Since you're using `stat="identity"` ggplot has no way to compute any reasonable error bars unless you want to do something weird like specify that they're some percentage of the bar height (might make sense if you have Poisson distributed values, but otherwise...). ...
written 1 day ago by Devon Ryan73k
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Comment: C: error bar in boxplot ggplot2
... How should the error values be derived? ...
written 2 days ago by Devon Ryan73k
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Answer: A: Not able to access galaxy ftp
... In general, you'll want to post Galaxy questions on [the galaxy site](http://biostar.usegalaxy.org). Anyway, you're not the only one experiencing this (I just tried), I'll alert the Galaxy admins so they can have a look. Note that I wouldn't expect anything to get fixed until Monday morning east co ...
written 2 days ago by Devon Ryan73k
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Comment: C: HISAT2 V.S. STAR
... You can get normalized counts from DESeq2, so either use them directly or convert them to FPKMs or just divide by transcript length if you want some sort of length-normalized value. ...
written 2 days ago by Devon Ryan73k

Latest awards to Devon Ryan

Teacher 19 hours ago, created an answer with at least 3 up-votes. For A: Concatenate Two .Fasta Files Into One
Scholar 19 hours ago, created an answer that has been accepted. For A: How To Create A Bigwig File And Display It
Appreciated 19 hours ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 1 day ago, created an answer with at least 3 up-votes. For A: Concatenate Two .Fasta Files Into One
Scholar 2 days ago, created an answer that has been accepted. For A: How To Create A Bigwig File And Display It
Scholar 4 days ago, created an answer that has been accepted. For A: How To Create A Bigwig File And Display It
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Concatenate Two .Fasta Files Into One
Scholar 5 days ago, created an answer that has been accepted. For A: How To Create A Bigwig File And Display It
Scholar 5 days ago, created an answer that has been accepted. For A: How To Create A Bigwig File And Display It
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: Concatenate Two .Fasta Files Into One
Scholar 14 days ago, created an answer that has been accepted. For A: detailed explanation of Insert Size
Teacher 15 days ago, created an answer with at least 3 up-votes. For A: Normalizing Rna-Seq Data Using Ercc Spike-In
Teacher 15 days ago, created an answer with at least 3 up-votes. For A: Bwa Mem: How To Specify The Fastq Phred Format?
Good Answer 20 days ago, created an answer that was upvoted at least 5 times. For A: Alignment and mapping
Scholar 20 days ago, created an answer that has been accepted. For A: detailed explanation of Insert Size
Commentator 20 days ago, created a comment with at least 3 up-votes. For C: Perl Script To Make Statistics Of Mirna Abundances For Many Samples
Teacher 21 days ago, created an answer with at least 3 up-votes. For A: Bwa Mem: How To Specify The Fastq Phred Format?
Teacher 22 days ago, created an answer with at least 3 up-votes. For A: Bwa Mem: How To Specify The Fastq Phred Format?
Teacher 22 days ago, created an answer with at least 3 up-votes. For A: Bwa Mem: How To Specify The Fastq Phred Format?
Commentator 22 days ago, created a comment with at least 3 up-votes. For C: Perl Script To Make Statistics Of Mirna Abundances For Many Samples
Scholar 24 days ago, created an answer that has been accepted. For A: detailed explanation of Insert Size
Scholar 25 days ago, created an answer that has been accepted. For A: detailed explanation of Insert Size
Good Answer 25 days ago, created an answer that was upvoted at least 5 times. For A: Alignment and mapping
Scholar 25 days ago, created an answer that has been accepted. For A: detailed explanation of Insert Size
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: Bwa Mem: How To Specify The Fastq Phred Format?

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