Admin: Devon Ryan

gravatar for Devon Ryan
Devon Ryan86k
Reputation:
86,180
Status:
Trusted
Location:
Freiburg, Germany
Twitter:
dpryan79
Scholar ID:
Google Scholar Page
Last seen:
6 hours ago
Joined:
5 years, 8 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 • 9,746 results • page 1 of 975 • next >
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Comment: C: What's the difference of FPKM generated by htseq and stringtie?
... Without further information it's impossible for anyone to know. ...
written 6 hours ago by Devon Ryan86k
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Comment: C: one gene one enzyme
... To provide a forum for pure biology questions. ...
written 2 days ago by Devon Ryan86k
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Comment: C: Genome Index and Alignment- STAR
... You only need the BAM file, I don't think it needs to be indexed. Do not use cufflinks, use stringTie. ...
written 3 days ago by Devon Ryan86k
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Comment: C: STAR alignment error: quantmod not found
... Your command has a random space or a missing `\` somewhere that you're not showing us. Write it all on one line without any `\`. ...
written 3 days ago by Devon Ryan86k
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Answer: A: STAR alignment error: quantmod not found
... `-- genomeDir` has a space in it. ...
written 3 days ago by Devon Ryan86k
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Comment: C: Genome Index and Alignment- STAR
... Yes, you can delete them ...
written 5 days ago by Devon Ryan86k
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Answer: A: Error: Could not find Bowtie 2 index files (splice-mismatch.*.bt2)
... You have a space in `-- splice-mismatch`. As mentioned in the comment, you should not be using tophat for anything. ...
written 5 days ago by Devon Ryan86k
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Comment: C: Genome Index and Alignment- STAR
... Those directories should be empty after it's done. The sorted BAM file is in the output directory you specified. STAR is a bit bad at cleaning up after itself, so you'll see a bunch of `_STAR*` folder sitting about that you can delete. The toplevel fasta should include all of the chromosomes anyway ...
written 6 days ago by Devon Ryan86k
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Comment: C: 'Error: Unable to open file test1.bed. Exiting' , Bedtools help
... Most likely either there's a typo in the command (you mistyped the file name) or the user you're running bedtools with doesn't have read permission. ...
written 6 days ago by Devon Ryan86k
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Answer: A: Tophat problem - R1 and R2 reads mapped to different strandeds of viral genome
... Don't use tophat2 any more. R1 and R2 will always map to opposing strands given how Illumina sequencing works. Note however that orientation of read 2 dictates the strand from which the RNA that was sequenced arose. So if you have a bunch of R2 reads on the - strand and R1 on the + strand then gen ...
written 9 days ago by Devon Ryan86k

Latest awards to Devon Ryan

Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Where Is Mirna Binding Site On Mrna ?
Commentator 8 days ago, created a comment with at least 3 up-votes. For C: Bwa Mem Method For Mapping, With Or Without Trimming Reads?
Appreciated 11 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Appreciated 14 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Commentator 14 days ago, created a comment with at least 3 up-votes. For C: Bwa Mem Method For Mapping, With Or Without Trimming Reads?
Teacher 18 days ago, created an answer with at least 3 up-votes. For A: Bwa Mem: How To Specify The Fastq Phred Format?
Teacher 18 days ago, created an answer with at least 3 up-votes. For A: Deseq Vs Edger..Filtering Read Counts.
Appreciated 19 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Commentator 21 days ago, created a comment with at least 3 up-votes. For C: Bwa Mem Method For Mapping, With Or Without Trimming Reads?
Teacher 24 days ago, created an answer with at least 3 up-votes. For A: Deseq Vs Edger..Filtering Read Counts.
Scholar 24 days ago, created an answer that has been accepted. For A: BWA-MEM Syntax Understanding
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: Deseq Vs Edger..Filtering Read Counts.
Good Answer 25 days ago, created an answer that was upvoted at least 5 times. For A: Deseq Vs Edger..Filtering Read Counts.
Teacher 26 days ago, created an answer with at least 3 up-votes. For A: Rna-Seq Library Design With Different Sequencing Depth
Teacher 26 days ago, created an answer with at least 3 up-votes. For A: Bwa Mem: How To Specify The Fastq Phred Format?
Scholar 4 weeks ago, created an answer that has been accepted. For A: BWA-MEM Syntax Understanding
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?
Appreciated 4 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Appreciated 4 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Scholar 4 weeks ago, created an answer that has been accepted. For A: BWA-MEM Syntax Understanding
Appreciated 5 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Rna-Seq Library Design With Different Sequencing Depth
Scholar 5 weeks ago, created an answer that has been accepted. For A: BWA-MEM Syntax Understanding
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Rna-Seq Library Design With Different Sequencing Depth
Appreciated 5 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs

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