Admin: Devon Ryan

gravatar for Devon Ryan
Devon Ryan62k
Reputation:
61,700
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Trusted
Location:
Freiburg, Germany
Twitter:
dpryan79
Scholar ID:
Google Scholar Page
Last seen:
19 seconds ago
Joined:
3 years, 11 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 • 7,428 results • page 1 of 743 • next >
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Comment: C: Main difference between RSEM and k-mer based quantification methods
... The answer to (1) is covered in the salmon/kallisto papers. ...
written 17 hours ago by Devon Ryan62k
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Comment: C: Why Ribo-seq not as popular as RNA-seq?
... If you're willing to put in the extra effort then sure. ...
written 1 day ago by Devon Ryan62k
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Comment: C: DESeq work flow in Galaxy
... [Here you go](https://www.dropbox.com/s/jxo59wkxu0xxnb8/Bju.gene.gtf.gz?dl=0). Make sure you explicitly label the file type as "gtf" when you upload it to Galaxy. ...
written 1 day ago by Devon Ryan62k
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Answer: A: Why Ribo-seq not as popular as RNA-seq?
... Ribo-seq is a much more complicated experiment. Further, you won't get any non-coding species in Ribo-seq. RNAseq is cheap and easy, though I wouldn't be surprised if Ribo-seq becomes a bit more popular over time. ...
written 1 day ago by Devon Ryan62k
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Answer: A: how to get Homo_sapiens.GRCh38.84.bed file
... `awk '{if($3 != "gene") print $0}' Homo_sapiens.GRCh38.84.gtf | grep -v "^#" | gtfToGenePred /dev/stdin /dev/stdout | genePredToBed stdin Homo_sapiens.GRCh38.84.bed` You can download the two tools from UCSC. If you're curious, this is from [here](https://github.com/maxplanck-ie/data_repository/blo ...
written 2 days ago by Devon Ryan62k
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Comment: C: DESeq work flow in Galaxy
... Either that species lacks UTRs or it's unknown where they are. So try using `CDS` instead of `exon`. Note that I'm not sure how well htseq-count handles GFF files, so if that doesn't work then just post a comment here and I'll make a proper GTF file for you. ...
written 2 days ago by Devon Ryan62k
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Comment: C: Invariant base quality calls
... Look at the read names, at least SRR5099289 was preprocessed. ...
written 3 days ago by Devon Ryan62k
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Comment: C: Invariant base quality calls
... Yes, one should provide raw data to SRA, but this is far from the first case where someone didn't do that. I would suggest contacting whoever is listed as the submitter for the dataset first. Hopefully they still have the raw data... ...
written 3 days ago by Devon Ryan62k
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Comment: C: Invariant base quality calls
... It looks incredibly likely that they preprocessed the data before upload. ...
written 4 days ago by Devon Ryan62k
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Comment: C: RNA Seq analysis of virally infected cells
... "Variant" as in the common English language meaning of the word, nothing to do with what you're apparently thinking of. You can subset a DESeqDataset object. If you only care about the viral genes, then just look at them but use the host genes to set the size factors. ...
written 4 days ago by Devon Ryan62k

Latest awards to Devon Ryan

Teacher 9 hours ago, created an answer with at least 3 up-votes. For A: R: Merge Duplicates In Column In Data.Frame By Condition In Another Column
Scholar 2 days ago, created an answer that has been accepted. For A: Group The Data In Python
Teacher 2 days ago, created an answer with at least 3 up-votes. For A: R: Merge Duplicates In Column In Data.Frame By Condition In Another Column
Good Answer 4 days ago, created an answer that was upvoted at least 5 times. For A: How to extract unique mapped results from Bowtie2 bam results?
Scholar 4 days ago, created an answer that has been accepted. For A: Group The Data In Python
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: R: Merge Duplicates In Column In Data.Frame By Condition In Another Column
Commentator 5 days ago, created a comment with at least 3 up-votes. For C: Will you critique/rate my mRNA seq alignment analysis?
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: R: Merge Duplicates In Column In Data.Frame By Condition In Another Column
Commentator 8 days ago, created a comment with at least 3 up-votes. For C: Will you critique/rate my mRNA seq alignment analysis?
Scholar 8 days ago, created an answer that has been accepted. For A: Group The Data In Python
Scholar 9 days ago, created an answer that has been accepted. For A: Group The Data In Python
Appreciated 9 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Appreciated 10 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: R: Merge Duplicates In Column In Data.Frame By Condition In Another Column
Scholar 13 days ago, created an answer that has been accepted. For A: Group The Data In Python
Scholar 13 days ago, created an answer that has been accepted. For A: Group The Data In Python
Appreciated 17 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Scholar 19 days ago, created an answer that has been accepted. For A: Group The Data In Python
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: R: Merge Duplicates In Column In Data.Frame By Condition In Another Column
Teacher 21 days ago, created an answer with at least 3 up-votes. For A: R: Merge Duplicates In Column In Data.Frame By Condition In Another Column
Teacher 21 days ago, created an answer with at least 3 up-votes. For A: R: Merge Duplicates In Column In Data.Frame By Condition In Another Column
Commentator 21 days ago, created a comment with at least 3 up-votes. For C: Will you critique/rate my mRNA seq alignment analysis?
Scholar 21 days ago, created an answer that has been accepted. For A: Group The Data In Python
Teacher 22 days ago, created an answer with at least 3 up-votes. For A: Tophat Vs. Bowtie: Quality Scores
Teacher 22 days ago, created an answer with at least 3 up-votes. For A: R: Merge Duplicates In Column In Data.Frame By Condition In Another Column

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