Admin: Devon Ryan

gravatar for Devon Ryan
Devon Ryan92k
Reputation:
92,030
Status:
Trusted
Location:
Freiburg, Germany
Twitter:
dpryan79
Scholar ID:
Google Scholar Page
Last seen:
17 hours ago
Joined:
6 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 • 10,107 results • page 1 of 1011 • next >
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Answer: A: Difference between abundance and counts in RNA-Seq
... A count is simply that, a count of reads on some feature. An abundance is a more biologically meaningful (though not necessarily statistically useful) quantification of expression of a gene or transcript that is normalized in some way. Most commonly in this is TPM or some variant of that, but it cou ...
written 17 hours ago by Devon Ryan92k
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Comment: C: deepTools cluster information?
... DeepTools cares about regions so it will typically ignore their names, which tend to be non-existent. ...
written 18 hours ago by Devon Ryan92k
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Comment: C: bcl2fastq can't find config.xml
... Why not use bcl2fastq2? bcl2fastq 1.8.4 has been deprecated for years. ...
written 18 hours ago by Devon Ryan92k
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Answer: A: DiffBind without replicates
... There are no statistically reliable methods that can be used to find differential peaks without replicates. ...
written 18 hours ago by Devon Ryan92k
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Comment: C: Question about featureCounts
... When in doubt, have a look in IGV (make sure to load the GTF you're using) and maybe have featureCounts output the SAM file with reads annotated according to their feature assignment. Then you can debug why reads are being assigned the way they are. ...
written 13 days ago by Devon Ryan92k
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Comment: C: Question about featureCounts
... The first command isn't counting per-exon, it's counting reads/pairs where at least one overlaps a gene's exons. In short, the first command is the standard command for RNA-seq and uses the default values for everything. If one wanted to count per-exon, one would need to change the `-g` option. ...
written 14 days ago by Devon Ryan92k
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Comment: C: Could you explain the difference between STAR, KALLISTO, SALMON etc. to experime
... Are you able to make the data public? It'd be much easier to figure out what's going on then. Note that knocked out genes are often still highly expressed, they're just not translated. ...
written 15 days ago by Devon Ryan92k
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Comment: C: Could you explain the difference between STAR, KALLISTO, SALMON etc. to experime
... Pseudoaligners are generally quite reliable, you may simply have one of the cases where they're not. That remains to be seen. ...
written 15 days ago by Devon Ryan92k
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Comment: C: Could you explain the difference between STAR, KALLISTO, SALMON etc. to experime
... When things like that happen it's good to get a BAM file. My guess is that the KO is deleting a single exon and that the recycling of the resulting non-sense transcript is simply lower in some of your samples. Alternatively, if there are paralogs then perhaps they really are messing up the pseudoali ...
written 15 days ago by Devon Ryan92k
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Comment: C: Is it okay to use deeptools bamCompare (SES normalization) for comparisons acros
... Cross-posted on bioinfo.SE, where I've already replied: https://bioinformatics.stackexchange.com/questions/10541/is-it-okay-to-use-deeptools-bamcompare-ses-normalization-for-comparisons-acros ...
written 16 days ago by Devon Ryan92k

Latest awards to Devon Ryan

Appreciated 2 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Good Answer 2 days ago, created an answer that was upvoted at least 5 times. For A: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Appreciated 2 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Appreciated 5 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
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: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Appreciated 7 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Scholar 8 days ago, created an answer that has been accepted. For A: Differential expression with leave one out?
Scholar 8 days ago, created an answer that has been accepted. For C: .bam format is not enough for mapped long reads
Scholar 8 days ago, created an answer that has been accepted. For A: How To Create A Bigwig File And Display It
Scholar 8 days ago, created an answer that has been accepted. For A: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Scholar 9 days ago, created an answer that has been accepted. For A: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Scholar 12 days ago, created an answer that has been accepted. For A: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Appreciated 15 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 23 days ago, created an answer with at least 3 up-votes. For A: Fields In The Vcf File
Commentator 25 days ago, created a comment with at least 3 up-votes. For C: Bwa Mem Method For Mapping, With Or Without Trimming Reads?
Scholar 25 days ago, created an answer that has been accepted. For A: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Teacher 26 days ago, created an answer with at least 3 up-votes. For A: Fields In The Vcf File
Pundit 28 days ago, created a comment with more than 10 votes. For C: SatckExchage/Area51 bioinformatics is back
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Fields In The Vcf File
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: Bwa Mem Method For Mapping, With Or Without Trimming Reads?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Fields In The Vcf File
Scholar 6 weeks ago, created an answer that has been accepted. For A: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Fields In The Vcf File
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

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