Admin: Devon Ryan

gravatar for Devon Ryan
Devon Ryan65k
Reputation:
65,480
Status:
Trusted
Location:
Freiburg, Germany
Twitter:
dpryan79
Scholar ID:
Google Scholar Page
Last seen:
17 minutes ago
Joined:
4 years, 2 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 • 7,782 results • page 1 of 779 • next >
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Comment: C: Using the Homer suite with conda
... macs2 doesn't have to be in the same environment. Have your shell command activate the appropriate one: shell: """ source activate my_macs2_env macs2 callpeak ... """ We do this all the time with environment modules. ...
written 2 hours ago by Devon Ryan65k
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Comment: C: Using the Homer suite with conda
... "Installing software" is typically listed as one of the top annoyances in bioinformatics :( ...
written 2 hours ago by Devon Ryan65k
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Answer: A: What are the most popular sequence alignment and sequence analysis tool/software
... Well, the most broadly used tool is probably blast. I suspect, however, that the question you asked is not the one you actually want to ask. ...
written 6 hours ago by Devon Ryan65k
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Answer: A: Using the Homer suite with conda
... You'd need to [update the bioconda recipe to fix this](https://github.com/bioconda/bioconda-recipes/issues/4033). As an aside, Homer is real mess to install and manage. I would encourage you to use something else if possible. ...
written 6 hours ago by Devon Ryan65k
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Answer: A: question regarding bioinformatics jobs in US
... You can always apply, but I suspect you won't have much success without either experience or a masters. ...
written 10 hours ago by Devon Ryan65k
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Answer: A: Detection of CNVs from vcf file
... Detecting CNVs from a VCF file would be what we call "a fool's errand". You'll want to use the BAM files instead. You can find appropriate tools if you google "CNV detection". ...
written 10 hours ago by Devon Ryan65k
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Comment: C: paired reads have different names (bwa-mem)
... Is it actually an error or just a warning? Did you download the fastq files or convert them with SRAtools? ...
written 10 hours ago by Devon Ryan65k
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Answer: A: RNA-Seq pipeline for clustering
... I would suggest that you ditch both cufflinks and stringTie and instead use featureCounts. Alternatively, one could also use salmon and skip the alignment step as well, if you don't care much about the exact alignments. In general, only use things like stringTie (never use cufflinks, stringTie is m ...
written 10 hours ago by Devon Ryan65k
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Comment: C: How to deal with RNA-SEQ samples with different number of raw reads?
... Correct, though it's not so much the difference between them as their ratio that ends up being a problem. ...
written 10 hours ago by Devon Ryan65k
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Answer: A: How to deal with RNA-SEQ samples with different number of raw reads?
... You only tend to run into problems once you get ~10x differences in depth. All common RNAseq tools (DESeq2, edgeR, limma/voom, etc.) will already properly normalize your data. ...
written 11 hours ago by Devon Ryan65k

Latest awards to Devon Ryan

Teacher 1 hour 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 6 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 1 day ago, created an answer that has been accepted. For A: Group The Data In Python
Appreciated 1 day ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Scholar 2 days ago, created an answer that has been accepted. For A: Group The Data In Python
Teacher 3 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 4 days ago, created an answer that has been accepted. For A: Group The Data In Python
Teacher 4 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 4 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 4 days ago, created an answer that has been accepted. For A: Group The Data In Python
Good Answer 5 days ago, created an answer that was upvoted at least 5 times. For A: How to extract unique mapped results from Bowtie2 bam results?
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: Why does biomart return multiple Entrez IDs
Teacher 6 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 7 days ago, created an answer that has been accepted. For A: Group The Data In Python
Scholar 7 days ago, created an answer that has been accepted. For A: How To Create A Bigwig File And Display It
Teacher 7 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
Appreciated 9 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 12 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 12 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
Appreciated 12 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Scholar 13 days ago, created an answer that has been accepted. For A: Group The Data In Python
Teacher 13 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 13 days ago, created an answer with at least 3 up-votes. For A: Tophat Vs. Bowtie: Quality Scores
Teacher 13 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 14 days ago, created an answer that was upvoted at least 5 times. For A: How to extract unique mapped results from Bowtie2 bam results?

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