Admin: Devon Ryan

gravatar for Devon Ryan
Devon Ryan71k
Reputation:
71,260
Status:
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Location:
Freiburg, Germany
Twitter:
dpryan79
Scholar ID:
Google Scholar Page
Last seen:
13 minutes ago
Joined:
4 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

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Comment: C: Error : samtools tview
... XRef: https://github.com/samtools/samtools/issues/728 ...
written 45 minutes ago by Devon Ryan71k
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Comment: C: Strange MA plot from DESeq2
... At this point I haven't a clue what's going on. I suspect there's simply something installed incorrectly on your system. I suggest you post this on the [bioconductor site](http://support.bioconductor.org) and wait for Mike Love (the DESeq2 author) to reply. Perhaps he has more insight as to where th ...
written 18 hours ago by Devon Ryan71k
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Answer: A: RNA STAR error on Gallaxy
... You should post this sort of error [on the galaxy site](https://biostar.usegalaxy.org). The likely cause of this is the chromosome name mismatch you referred to. Given the file path you mentioned I'm guessing you're using the main usegalaxy.org site. That seems to use UCSC chromosome names (e.g., ` ...
written 18 hours ago by Devon Ryan71k
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Comment: C: setting Coldata levels in Deseq2
... Yes, `sampleCondition` rather than `sampleTable`. For the results of other comparisons, see `help(results)`. ...
written 1 day ago by Devon Ryan71k
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Answer: A: RNAseq bad PCA, a differential expression analysis killer ?
... You're never guaranteed that your groups will cluster nicely in PCA. If they do, you likely have a large effect size. If they don't you likely have a small effect size (or some issue). With the stuff I did as a post-doc, I expected very subtle differences between groups so I was never surprised to n ...
written 1 day ago by Devon Ryan71k
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Answer: A: STAR/ Bowtie2: number of matched base
... The simplest thing to change in bowtie2 is `--score-min`. STAR is vastly more configurable than most any other aligner, so don't expect to be able to tweak other tools as much. ...
written 1 day ago by Devon Ryan71k
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Comment: C: EdgeR Paired-Sample Test
... Correct, it'd be `coef=3` in that case. ...
written 1 day ago by Devon Ryan71k
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Comment: C: setting Coldata levels in Deseq2
... I put the missing `)` back, I may have accidentally deleted it when I reformatted this post. ...
written 1 day ago by Devon Ryan71k
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Answer: A: Lnc RNA,RNA Seq
... The `l` in lncRNAs stands for `long`, which in this case is >200 bases. Given that, an sRNAseq library prep would get rid of most lncRNAs. You need a ribo-depleted RNAseq dataset (the typical prep uses polyA selection, which will exclude some non-coding RNAs). ...
written 1 day ago by Devon Ryan71k
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Comment: C: Is there any read-mapping package that could map only the first half or the seco
... Why not just map everything as is and allow a LOT of soft-clipping? The soft-clipped portion is then likely to be your insert. ...
written 1 day ago by Devon Ryan71k

Latest awards to Devon Ryan

Scholar 5 hours ago, created an answer that has been accepted. For A: detailed explanation of Insert Size
Teacher 10 hours ago, created an answer with at least 3 up-votes. For A: detailed explanation of Insert Size
Teacher 1 day ago, created an answer with at least 3 up-votes. For A: How To Generate Synthetic Read Data From An Existing Fasta
Teacher 1 day ago, created an answer with at least 3 up-votes. For A: detailed explanation of Insert Size
Teacher 1 day ago, created an answer with at least 3 up-votes. For A: detailed explanation of Insert Size
Scholar 1 day ago, created an answer that has been accepted. For A: detailed explanation of Insert Size
Teacher 2 days ago, created an answer with at least 3 up-votes. For A: detailed explanation of Insert Size
Scholar 2 days ago, created an answer that has been accepted. For A: detailed explanation of Insert Size
Scholar 5 days ago, created an answer that has been accepted. For A: detailed explanation of Insert Size
Appreciated 7 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Scholar 7 days ago, created an answer that has been accepted. For A: detailed explanation of Insert Size
Appreciated 7 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 7 days ago, created an answer with at least 3 up-votes. For A: detailed explanation of Insert Size
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: detailed explanation of Insert Size
Scholar 8 days ago, created an answer that has been accepted. For A: detailed explanation of Insert Size
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: detailed explanation of Insert Size
Scholar 8 days ago, created an answer that has been accepted. For A: detailed explanation of Insert Size
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Fpkm To Transcript Quantification
Appreciated 9 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 11 days ago, created an answer with at least 3 up-votes. For A: Fpkm To Transcript Quantification
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Fpkm To Transcript Quantification
Scholar 21 days ago, created an answer that has been accepted. For A: Why does GFF prepared using dexseq_prepare_annotation shows different exon numbe
Teacher 24 days ago, created an answer with at least 3 up-votes. For A: Fpkm To Transcript Quantification
Good Answer 26 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

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