User: Devon Ryan

gravatar for Devon Ryan
Devon Ryan1.7k
Reputation:
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Location:
Germany
Twitter:
dpryan79
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an hour ago
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2 years, 6 months ago
Email:
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Bioinformatician / data manager at the Max Planck Institute for Immunobiology and Epigenetics in Freiburg, Germany. I'm one of the developers for deepTools (among other packages).

Posts by Devon Ryan

<prev • 305 results • page 1 of 31 • next >
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Comment: C: PEAR alternative for merging overlapping paired-end reads using Galaxy tools
... Make sure to do trimming on both files at the same time with a tool like trimmomatic or trim galore. Trimming the mates independently will cause problems like this. ...
written 4 days ago by Devon Ryan1.7k
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Comment: C: PEAR alternative for merging overlapping paired-end reads using Galaxy tools
... You'd need to post the error message. I'm curious what you expect to gain from merging reads if they're all expected to be complete overlaps. I would think it'd be simpler to take read 1 and be done with it. ...
written 5 days ago by Devon Ryan1.7k
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Answer: A: PEAR alternative for merging overlapping paired-end reads using Galaxy tools
... You can use the FLASH tool. ...
written 5 days ago by Devon Ryan1.7k
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Answer: A: fastqsanger to fastq
... Just download the files as they are, "fastqsanger" is just a Galaxy name for the type of fastq file that's produced by modern sequencing machines. ...
written 10 days ago by Devon Ryan1.7k
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Answer: A: Extracting files from sequencing core
... > I was wondering if there is a faster way to get them all onto my external hard drive? Give the sequencing facility your hard drive. They should be able to just copy everything on more quickly. > Once I get the data do I then need to change all of the file extensions to fastqsanger in orde ...
written 12 days ago by Devon Ryan1.7k
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Answer: A: PEAR removed from the tool list?
... This was announced yesterday [on twitter](https://twitter.com/galaxyproject/status/917806062048350209). You can use FLASh instead. ...
written 12 days ago by Devon Ryan1.7k
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Comment: C: BAM files on IGV look empty
... How big was the file when you downloaded it? ...
written 21 days ago by Devon Ryan1.7k
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Answer: A: DEseq2 collapseReplicates (Technical Replicates) function in Galaxy
... 1. Merge the technical replicates on their shared ID column 2. Sum the two columns of counts. 3. Select only the first ID column and the sum column You can use that as the input into DESeq2. In RNAseq, technical replicates are collapsed by simply adding their per-gene counts together. ...
written 21 days ago by Devon Ryan1.7k
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Answer: A: Is && needed in xml for seperating lines?
... `&&` isn't so much separating lines as it is separating commands. Have a look [here](https://github.com/fidelram/deepTools/blob/master/galaxy/wrapper/bamCompare.xml) for an example using `&&` to separate commands and nothing separating lines (the main command is split across many lin ...
written 21 days ago by Devon Ryan1.7k
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Comment: C: Trimmomatic data on Fastqc
... Please post the entire error message. ...
written 5 weeks ago by Devon Ryan1.7k

Latest awards to Devon Ryan

Scholar 3 months ago, created an answer that has been accepted. For A: Docker Galaxy Job conf file and SLURM
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