User: VY

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VY120
Reputation:
120
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Location:
United States
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1 month, 2 weeks ago
Joined:
2 years, 2 months ago
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k*******@kcl.ac.uk

Posts by VY

<prev • 45 results • page 1 of 5 • next >
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Change Tracking Id to Gene name
... Hello, I'm not sure if this is something that can be done in galaxy, but if anyone knows how to do it in R that would help aswell. I've run cuffdiff on my samples and I've selected the output count file function. When I look at my cuffdiff gene count tracking file, all the rows are under the trac ...
cuffdiff rnaseq rna-seq written 7 weeks ago by VY120 • updated 6 weeks ago by Jennifer Hillman Jackson21k
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Comment: C: ChIP-seq sequence data sources
... Hello, again, to my knowledge, ChIPseq will not predict nucleosome spreading. Off the top of my head the only way you could INFER that from ChIPseq is if you have ChIP data done on Polycomb and/or Trithorax proteins that are known to compact or relax chromatin (e.g Ring1B and MLL1 respectively -plea ...
written 4 months ago by VY120
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Answer: A: chip seq data
... If you're looking at nucleosome positioning you probably need ATAC-seq data and/or DNAse -seq data etc. ChIP-seq won't give you that unless you are looking at a specific nucleosome remodeling protein (or any protein for that matter). Also specifying from what bovine tissue you want would be most hel ...
written 4 months ago by VY120
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Comment: A: FASTQ Groomer error
... Hello, It's probably an issue on their end, alot of tools have been outputting the same error recently. Val ...
written 5 months ago by VY120
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Error 28: No space left on Device
... Hello, I try to run a number of things (bamCoverage, computeMatrix, PlotProfile etc) under the NGS Deep tools on Galaxy main and they all keep coming back with different errors, even though they were working yesterday on exactly the same data files. The main error I keep getting from them is: "No ...
server space usegalaxy.org cluster error written 5 months ago by VY120 • updated 5 months ago by Jennifer Hillman Jackson21k
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Answer: A: TopHat alignment of RNA seq data
... Hi Diana, As everything you can't really let the tools run on autopilot without knowing what it is you're doing or why. My suggestion would be read the documentation and actually get a feel about what each parameter does. If you're pushed for time to get some results or need to confirm a hypothesi ...
written 5 months ago by VY120
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MACS2 undefined Error
... Hello Galaxy team, I'm running some pretty standard peak calling using MACS2 and get the following error as the job fails : > This job failed for reasons that could not be determined. Please click > the bug icon to report this problem if you need help. Is there a tool issue? I've tried doin ...
macs2 chip chipseq written 5 months ago by VY120 • updated 5 months ago by Jennifer Hillman Jackson21k
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Answer: A: Remote job server indicated a problem running or monitoring this job.
... Hello, I had this reported via galaxy as a bug. Got an email response back from Jen that there was a cluster error that should be fixed now. Try re-running your jobs. BW Val ...
written 5 months ago by VY120
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Tool error "Remote job server indicated a problem running or monitoring this job"
... Hello Galaxy team, I'm trying to align some fastq files to mm10 and the job crashes with this description: Tool Error : Remote job server indicated a problem running or monitoring this job. Any ideas? thanks, Best wishes, V ...
bowtie2 usegalaxy.org job tool error written 5 months ago by VY120 • updated 5 months ago by Jennifer Hillman Jackson21k
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Answer: C: Can't obtain overlapping Peaks
... Hi Jen, Did some digging in my datasets and the issue doesn't seem to be with the intersect tool afterall but with MACS2. For some reason if I look at the attributes of my "summits in bed" MACS2 output. The column labels (start, end, strand etc) and the column numbers automatically detected don't s ...
written 5 months ago by VY120

Latest awards to VY

Scholar 4 months ago, created an answer that has been accepted. For A: chip seq data

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