Admin: Devon Ryan

gravatar for Devon Ryan
Devon Ryan90k
Reputation:
90,410
Status:
Trusted
Location:
Freiburg, Germany
Twitter:
dpryan79
Scholar ID:
Google Scholar Page
Last seen:
22 hours ago
Joined:
6 years, 3 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 • 10,041 results • page 1 of 1005 • next >
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Comment: C: Remove HB genes and recalculate read depth
... Sum each sample. ...
written 1 day ago by Devon Ryan90k
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Comment: C: Remove HB genes and recalculate read depth
... You'll need to decrease that to ~20 million if you start with a counts matrix, which would approximately match. ...
written 1 day ago by Devon Ryan90k
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Comment: C: how can I align several fastq files with hisat2 and get htseq-count
... I strongly recommend that you not use bash scripting and instead use something more scalable and controllable like snakemake. ...
written 1 day ago by Devon Ryan90k
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Comment: C: Nanopore data to gtf/gff file
... Why not use stringTie? Note that minimap2 doesn't output a GTF. ...
written 1 day ago by Devon Ryan90k
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Comment: C: Remove HB genes and recalculate read depth
... Why not just subtract whatever maps to HB from the total? What kind of summarization are you going for? With DESeq2 you can just exclude it from the DESeqDataSet. ...
written 1 day ago by Devon Ryan90k
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Comment: C: How to create own SRAdb
... That's incredibly annoying, I had presumed that since you were at NIH you'd have more direct access. ...
written 3 days ago by Devon Ryan90k
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Comment: C: How to create own SRAdb
... They have direct access to SRA, you might just ask them to update the file. I've sent Sean Davis a tweet to ask for his input here. ...
written 3 days ago by Devon Ryan90k
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Comment: C: Convert fasta headers to GFF
... That spec shows how poorly defined GFF is for holding gene information. GFF is very flexible, which is the exact opposite of what's needed. Where should one find gene IDs and names? Are they the IDs (presumably)? Half the time with GFF files encountered in the wild those are just meaningless running ...
written 3 days ago by Devon Ryan90k
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Comment: C: Peak calling using spp package
... SPP is relatively obscure, with few people outside of ENCODE ever using it. Try a more common peak caller like MACS2 or SICER. ...
written 3 days ago by Devon Ryan90k
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Answer: A: Convert fasta headers to GFF
... 1. Use a GTF file instead, GFF is an awkward poorly supported "format". 2. CHR_HSCHR7_2_CTG6 shouldn't be in your fasta file, you've incorrectly used the "top level" fasta file, when you should be using the [primary assembly](ftp://ftp.ensembl.org/pub/release-96/fasta/homo_sapiens/dna/Homo_sapiens.G ...
written 3 days ago by Devon Ryan90k

Latest awards to Devon Ryan

Teacher 3 days ago, created an answer with at least 3 up-votes. For A: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Popular Question 6 days ago, created a question with more than 1,000 views. For BWA 0.7.11 is out, supports ALT contigs
Good Answer 7 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 8 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Scholar 8 days ago, created an answer that has been accepted. For A: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Good Answer 14 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 14 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Popular Question 15 days ago, created a question with more than 1,000 views. For BWA 0.7.11 is out, supports ALT contigs
Appreciated 18 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Appreciated 19 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Appreciated 20 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 22 days ago, created an answer with at least 3 up-votes. For A: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Scholar 22 days ago, created an answer that has been accepted. For A: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Scholar 24 days ago, created an answer that has been accepted. For A: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Appreciated 4 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Scholar 5 weeks ago, created an answer that has been accepted. For A: Differential expression with leave one out?
Scholar 5 weeks ago, created an answer that has been accepted. For A: Count antisense transcripts using STAR --quantMode
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Where Is Mirna Binding Site On Mrna ?
Appreciated 7 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs

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